diff --git a/server/src/__tests__/environment-runtime.test.ts b/server/src/__tests__/environment-runtime.test.ts
index ffda21c61ee..292c32481e4 100644
--- a/server/src/__tests__/environment-runtime.test.ts
+++ b/server/src/__tests__/environment-runtime.test.ts
@@ -177,6 +177,13 @@ describeEmbeddedPostgres("environmentRuntimeService", () => {
         provider: "local_encrypted",
         value: config.privateKey,
       });
+      await secretService(db).createBinding({
+        companyId,
+        secretId: secret.id,
+        targetType: "environment",
+        targetId: environmentId,
+        configPath: "privateKeySecretRef",
+      });
       config = {
         ...config,
         privateKey: null,
@@ -548,6 +555,13 @@ describeEmbeddedPostgres("environmentRuntimeService", () => {
       driver: "sandbox",
       config: providerConfig,
     };
+    await secretService(db).createBinding({
+      companyId,
+      secretId: apiSecret.id,
+      targetType: "environment",
+      targetId: environment.id,
+      configPath: "apiKey",
+    });
     await environmentService(db).update(environment.id, {
       driver: "sandbox",
       name: environment.name,
diff --git a/server/src/__tests__/heartbeat-project-env.test.ts b/server/src/__tests__/heartbeat-project-env.test.ts
index 8490b04e418..55653be3692 100644
--- a/server/src/__tests__/heartbeat-project-env.test.ts
+++ b/server/src/__tests__/heartbeat-project-env.test.ts
@@ -17,6 +17,17 @@ describe("resolveExecutionRunAdapterConfig", () => {
         other: "value",
       },
       secretKeys: new Set(["AGENT_SECRET"]),
+      manifest: [
+        {
+          configPath: "env.AGENT_SECRET",
+          envKey: "AGENT_SECRET",
+          secretId: "secret-agent",
+          secretKey: "agent-secret",
+          version: 1,
+          provider: "local_encrypted",
+          outcome: "success",
+        },
+      ],
     });
     const resolveEnvBindings = vi.fn().mockResolvedValue({
       env: {
@@ -24,6 +35,17 @@ describe("resolveExecutionRunAdapterConfig", () => {
         PROJECT_ONLY: "project-only",
       },
       secretKeys: new Set(["PROJECT_SECRET"]),
+      manifest: [
+        {
+          configPath: "env.PROJECT_SECRET",
+          envKey: "PROJECT_SECRET",
+          secretId: "secret-project",
+          secretKey: "project-secret",
+          version: 1,
+          provider: "local_encrypted",
+          outcome: "success",
+        },
+      ],
     });
 
     const result = await resolveExecutionRunAdapterConfig({
@@ -45,12 +67,19 @@ describe("resolveExecutionRunAdapterConfig", () => {
       },
     });
     expect(Array.from(result.secretKeys).sort()).toEqual(["AGENT_SECRET", "PROJECT_SECRET"]);
+    expect(result.secretManifest.map((entry) => entry.secretId).sort()).toEqual([
+      "secret-agent",
+      "secret-project",
+    ]);
+    expect(JSON.stringify(result.secretManifest)).not.toContain("agent-only");
+    expect(JSON.stringify(result.secretManifest)).not.toContain("project-only");
   });
 
   it("skips project env resolution when the project has no bindings", async () => {
     const resolveAdapterConfigForRuntime = vi.fn().mockResolvedValue({
       config: { env: { AGENT_ONLY: "agent-only" } },
       secretKeys: new Set<string>(),
+      manifest: [],
     });
     const resolveEnvBindings = vi.fn();
 
@@ -65,6 +94,7 @@ describe("resolveExecutionRunAdapterConfig", () => {
     });
 
     expect(result.resolvedConfig.env).toEqual({ AGENT_ONLY: "agent-only" });
+    expect(result.secretManifest).toEqual([]);
     expect(resolveEnvBindings).not.toHaveBeenCalled();
   });
 });
diff --git a/server/src/routes/environments.ts b/server/src/routes/environments.ts
index fd7976cadae..5d1e306960d 100644
--- a/server/src/routes/environments.ts
+++ b/server/src/routes/environments.ts
@@ -17,6 +17,7 @@ import {
   projectService,
 } from "../services/index.js";
 import {
+  collectEnvironmentSecretRefs,
   normalizeEnvironmentConfigForPersistence,
   normalizeEnvironmentConfigForProbe,
   parseEnvironmentDriverConfig,
@@ -211,6 +212,11 @@ export function environmentRoutes(
       }),
     };
     const environment = await svc.create(companyId, input);
+    await secrets.syncSecretRefsForTarget(
+      companyId,
+      { targetType: "environment", targetId: environment.id },
+      await collectEnvironmentSecretRefs({ db, environment }),
+    );
     await logActivity(db, {
       companyId,
       actorType: actor.actorType,
@@ -320,6 +326,13 @@ export function environmentRoutes(
       res.status(404).json({ error: "Environment not found" });
       return;
     }
+    if (patch.config !== undefined || patch.driver !== undefined) {
+      await secrets.syncSecretRefsForTarget(
+        environment.companyId,
+        { targetType: "environment", targetId: environment.id },
+        await collectEnvironmentSecretRefs({ db, environment }),
+      );
+    }
     await logActivity(db, {
       companyId: environment.companyId,
       actorType: actor.actorType,
diff --git a/server/src/routes/plugins.ts b/server/src/routes/plugins.ts
index 35b60812609..e9f5667bfb2 100644
--- a/server/src/routes/plugins.ts
+++ b/server/src/routes/plugins.ts
@@ -73,6 +73,8 @@ import {
   requireLocalFolderDeclaration,
   setStoredLocalFolder,
 } from "../services/plugin-local-folders.js";
+import { extractSecretRefPathsFromConfig } from "../services/plugin-secrets-handler.js";
+import { secretService } from "../services/secrets.js";
 import { badRequest, forbidden, notFound, unauthorized, unprocessable } from "../errors.js";
 
 /** UI slot declaration extracted from plugin manifest */
@@ -1944,6 +1946,29 @@ export function pluginRoutes(
       const result = await registry.upsertConfig(plugin.id, {
         configJson: body.configJson,
       });
+      const secretRefsByPath = extractSecretRefPathsFromConfig(body.configJson, schema);
+      const secrets = secretService(db);
+      const refsByCompany = new Map<string, Array<{ secretId: string; configPath: string; versionSelector: "latest" }>>();
+      for (const secretRef of secretRefsByPath.keys()) {
+        const secret = await secrets.getById(secretRef);
+        if (!secret) continue;
+        const refs = refsByCompany.get(secret.companyId) ?? [];
+        for (const configPath of secretRefsByPath.get(secretRef) ?? []) {
+          refs.push({
+            secretId: secretRef,
+            configPath,
+            versionSelector: "latest",
+          });
+        }
+        refsByCompany.set(secret.companyId, refs);
+      }
+      for (const [companyId, refs] of refsByCompany) {
+        await secrets.syncSecretRefsForTarget(
+          companyId,
+          { targetType: "plugin", targetId: plugin.id },
+          refs,
+        );
+      }
       await logPluginMutationActivity(req, "plugin.config.updated", plugin.id, {
         pluginId: plugin.id,
         pluginKey: plugin.pluginKey,
diff --git a/server/src/services/environment-config.ts b/server/src/services/environment-config.ts
index 2c9bdf413b0..79b0c3a5933 100644
--- a/server/src/services/environment-config.ts
+++ b/server/src/services/environment-config.ts
@@ -9,6 +9,7 @@ import type {
   PluginEnvironmentConfig,
   PluginSandboxEnvironmentConfig,
   SandboxEnvironmentConfig,
+  SecretVersionSelector,
   SshEnvironmentConfig,
 } from "@paperclipai/shared";
 import { unprocessable } from "../errors.js";
@@ -226,6 +227,11 @@ async function resolveConfigSecretRefsForRuntime(input: {
   companyId: string;
   config: Record<string, unknown>;
   schema: Record<string, unknown> | null;
+  context: {
+    consumerId: string;
+    issueId?: string | null;
+    heartbeatRunId?: string | null;
+  };
 }): Promise<Record<string, unknown>> {
   const secrets = secretService(input.db);
   let nextConfig = { ...input.config };
@@ -234,15 +240,52 @@ async function resolveConfigSecretRefsForRuntime(input: {
     if (typeof current !== "string") continue;
     const trimmed = current.trim();
     if (!isUuidSecretRef(trimmed)) continue;
+    if (!input.context.consumerId) {
+      throw unprocessable("Runtime secret resolution requires an environment id");
+    }
     nextConfig = writeConfigValueAtPath(
       nextConfig,
       path,
-      await secrets.resolveSecretValue(input.companyId, trimmed, "latest"),
+      await secrets.resolveSecretValue(input.companyId, trimmed, "latest", {
+        consumerType: "environment",
+        consumerId: input.context.consumerId,
+        actorType: "system",
+        actorId: null,
+        issueId: input.context.issueId ?? null,
+        heartbeatRunId: input.context.heartbeatRunId ?? null,
+        configPath: path,
+      }),
     );
   }
   return nextConfig;
 }
 
+export async function collectEnvironmentSecretRefs(input: {
+  db: Db;
+  environment: Pick<Environment, "id" | "driver" | "config">;
+}): Promise<Array<{ secretId: string; configPath: string; versionSelector?: SecretVersionSelector }>> {
+  const parsed = parseEnvironmentDriverConfig(input.environment);
+  if (parsed.driver === "ssh" && parsed.config.privateKeySecretRef) {
+    return [{
+      secretId: parsed.config.privateKeySecretRef.secretId,
+      configPath: "privateKeySecretRef",
+      versionSelector: parsed.config.privateKeySecretRef.version ?? "latest",
+    }];
+  }
+  if (parsed.driver === "sandbox" && parsed.config.provider !== "fake") {
+    const schema = await getSandboxProviderConfigSchema(input.db, parsed.config.provider);
+    const refs: Array<{ secretId: string; configPath: string; versionSelector?: SecretVersionSelector }> = [];
+    for (const path of collectSecretRefPaths(schema)) {
+      const current = readConfigValueAtPath(parsed.config as Record<string, unknown>, path);
+      if (typeof current === "string" && isUuidSecretRef(current.trim())) {
+        refs.push({ secretId: current.trim(), configPath: path, versionSelector: "latest" });
+      }
+    }
+    return refs;
+  }
+  return [];
+}
+
 export function stripSandboxProviderEnvelope(config: SandboxEnvironmentConfig): Record<string, unknown> {
   const { provider: _provider, ...driverConfig } = config as Record<string, unknown>;
   return driverConfig;
@@ -442,10 +485,15 @@ export async function normalizeEnvironmentConfigForPersistence(input: {
 export async function resolveEnvironmentDriverConfigForRuntime(
   db: Db,
   companyId: string,
-  environment: Pick<Environment, "driver" | "config">,
+  environment: Pick<Environment, "driver" | "config"> & Partial<Pick<Environment, "id">>,
+  context?: { issueId?: string | null; heartbeatRunId?: string | null },
 ): Promise<ParsedEnvironmentConfig> {
   const parsed = parseEnvironmentDriverConfig(environment);
   const secrets = secretService(db);
+  const environmentId = environment.id;
+  if (parsed.driver === "ssh" && parsed.config.privateKeySecretRef && !environmentId) {
+    throw unprocessable("Runtime secret resolution requires an environment id");
+  }
 
   if (parsed.driver === "ssh" && parsed.config.privateKeySecretRef) {
     return {
@@ -456,6 +504,15 @@ export async function resolveEnvironmentDriverConfigForRuntime(
           companyId,
           parsed.config.privateKeySecretRef.secretId,
           parsed.config.privateKeySecretRef.version ?? "latest",
+          {
+            consumerType: "environment",
+            consumerId: environmentId!,
+            actorType: "system",
+            actorId: null,
+            issueId: context?.issueId ?? null,
+            heartbeatRunId: context?.heartbeatRunId ?? null,
+            configPath: "privateKeySecretRef",
+          },
         ),
       },
     };
@@ -469,6 +526,11 @@ export async function resolveEnvironmentDriverConfigForRuntime(
         companyId,
         config: parsed.config as Record<string, unknown>,
         schema: await getSandboxProviderConfigSchema(db, parsed.config.provider),
+        context: {
+          consumerId: environmentId!,
+          issueId: context?.issueId ?? null,
+          heartbeatRunId: context?.heartbeatRunId ?? null,
+        },
       }) as SandboxEnvironmentConfig,
     };
   }
diff --git a/server/src/services/environment-runtime.ts b/server/src/services/environment-runtime.ts
index 733d03b2951..292d630dcfd 100644
--- a/server/src/services/environment-runtime.ts
+++ b/server/src/services/environment-runtime.ts
@@ -228,7 +228,10 @@ function createSshEnvironmentDriver(db: Db): EnvironmentRuntimeDriver {
     driver: "ssh",
 
     async acquireRunLease(input) {
-      const parsed = await resolveEnvironmentDriverConfigForRuntime(db, input.companyId, input.environment);
+      const parsed = await resolveEnvironmentDriverConfigForRuntime(db, input.companyId, input.environment, {
+        issueId: input.issueId,
+        heartbeatRunId: input.heartbeatRunId,
+      });
       if (parsed.driver !== "ssh") {
         throw new Error(`Expected SSH environment config for driver "${input.environment.driver}".`);
       }
@@ -346,6 +349,7 @@ function createSandboxEnvironmentDriver(
     const metadataConfig = sandboxConfigFromLeaseMetadataLoose(input.lease);
     if (metadataConfig && metadataConfig.provider === input.provider) {
       const parsed = await resolveEnvironmentDriverConfigForRuntime(db, input.lease.companyId, {
+        id: input.environment.id,
         driver: "sandbox",
         config: sandboxConfigForLeaseMetadata(metadataConfig),
       });
@@ -381,7 +385,10 @@ function createSandboxEnvironmentDriver(
 
     async acquireRunLease(input) {
       const storedParsed = parseEnvironmentDriverConfig(input.environment);
-      const parsed = await resolveEnvironmentDriverConfigForRuntime(db, input.companyId, input.environment);
+      const parsed = await resolveEnvironmentDriverConfigForRuntime(db, input.companyId, input.environment, {
+        issueId: input.issueId,
+        heartbeatRunId: input.heartbeatRunId,
+      });
       if (parsed.driver !== "sandbox" || storedParsed.driver !== "sandbox") {
         throw new Error(`Expected sandbox environment config for driver "${input.environment.driver}".`);
       }
@@ -562,6 +569,7 @@ function createSandboxEnvironmentDriver(
 
       const parsed = metadataConfig
         ? await resolveEnvironmentDriverConfigForRuntime(db, input.lease.companyId, {
+            id: input.environment.id,
             driver: "sandbox",
             config: metadataConfig as unknown as Record<string, unknown>,
           })
diff --git a/server/src/services/heartbeat.ts b/server/src/services/heartbeat.ts
index 46eaa4142b1..29cdda9e1c5 100644
--- a/server/src/services/heartbeat.ts
+++ b/server/src/services/heartbeat.ts
@@ -335,7 +335,7 @@ export async function resolveExecutionRunAdapterConfig(input: {
   projectEnv: unknown;
   secretsSvc: RuntimeConfigSecretResolver;
 }) {
-  const { config: resolvedConfig, secretKeys } = await input.secretsSvc.resolveAdapterConfigForRuntime(
+  const { config: resolvedConfig, secretKeys, manifest } = await input.secretsSvc.resolveAdapterConfigForRuntime(
     input.companyId,
     input.executionRunConfig,
     input.agentId
@@ -364,7 +364,7 @@ export async function resolveExecutionRunAdapterConfig(input: {
             }
           : undefined,
       )
-    : { env: {}, secretKeys: new Set<string>() };
+    : { env: {}, secretKeys: new Set<string>(), manifest: [] };
   if (Object.keys(projectEnvResolution.env).length > 0) {
     resolvedConfig.env = {
       ...parseObject(resolvedConfig.env),
@@ -374,7 +374,11 @@ export async function resolveExecutionRunAdapterConfig(input: {
       secretKeys.add(key);
     }
   }
-  return { resolvedConfig, secretKeys };
+  return {
+    resolvedConfig,
+    secretKeys,
+    secretManifest: [...(manifest ?? []), ...(projectEnvResolution.manifest ?? [])],
+  };
 }
 
 export function extractMentionedSkillIdsFromSources(
@@ -7023,7 +7027,7 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
     });
     const configSnapshot = buildExecutionWorkspaceConfigSnapshot(mergedConfig, selectedEnvironmentId);
     const executionRunConfig = stripWorkspaceRuntimeFromExecutionRunConfig(mergedConfig);
-    const { resolvedConfig, secretKeys } = await resolveExecutionRunAdapterConfig({
+    const { resolvedConfig, secretKeys, secretManifest } = await resolveExecutionRunAdapterConfig({
       companyId: agent.companyId,
       agentId: agent.id,
       issueId,
@@ -7033,6 +7037,13 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
       projectEnv: projectContext?.env ?? null,
       secretsSvc,
     });
+    if (secretManifest.length > 0) {
+      context.paperclipSecrets = {
+        manifest: secretManifest,
+      };
+    } else {
+      delete context.paperclipSecrets;
+    }
     const runScopedMentionedSkillKeys = await resolveRunScopedMentionedSkillKeys({
       db,
       companyId: agent.companyId,
diff --git a/server/src/services/plugin-secrets-handler.ts b/server/src/services/plugin-secrets-handler.ts
index b80ae187bda..8a3ada13d77 100644
--- a/server/src/services/plugin-secrets-handler.ts
+++ b/server/src/services/plugin-secrets-handler.ts
@@ -33,12 +33,11 @@
  * @see services/secrets.ts — secretService used by agent env bindings
  */
 
-import { eq, and, desc } from "drizzle-orm";
+import { eq } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
-import { companySecrets, companySecretVersions, pluginConfig } from "@paperclipai/db";
-import type { SecretProvider } from "@paperclipai/shared";
-import { getSecretProvider } from "../secrets/provider-registry.js";
+import { companySecrets, pluginConfig } from "@paperclipai/db";
 import { pluginRegistryService } from "./plugin-registry.js";
+import { secretService } from "./secrets.js";
 import {
   collectSecretRefPaths,
   isUuidSecretRef,
@@ -59,12 +58,6 @@ function secretNotFound(secretRef: string): Error {
   return err;
 }
 
-function secretVersionNotFound(secretRef: string): Error {
-  const err = new Error(`No version found for secret: ${secretRef}`);
-  err.name = "SecretVersionNotFoundError";
-  return err;
-}
-
 function invalidSecretRef(secretRef: string): Error {
   const err = new Error(`Invalid secret reference: ${secretRef}`);
   err.name = "InvalidSecretRefError";
@@ -86,8 +79,20 @@ export function extractSecretRefsFromConfig(
   configJson: unknown,
   schema?: Record<string, unknown> | null,
 ): Set<string> {
-  const refs = new Set<string>();
-  if (configJson == null || typeof configJson !== "object") return refs;
+  return new Set(extractSecretRefPathsFromConfig(configJson, schema).keys());
+}
+
+export function extractSecretRefPathsFromConfig(
+  configJson: unknown,
+  schema?: Record<string, unknown> | null,
+): Map<string, Set<string>> {
+  const refs = new Map<string, Set<string>>();
+  const addRef = (secretRef: string, path: string) => {
+    const existing = refs.get(secretRef) ?? new Set<string>();
+    existing.add(path);
+    refs.set(secretRef, existing);
+  };
+  if (configJson == null || typeof configJson !== "object") return new Map();
 
   const secretPaths = collectSecretRefPaths(schema);
 
@@ -96,7 +101,7 @@ export function extractSecretRefsFromConfig(
     for (const dotPath of secretPaths) {
       const current = readConfigValueAtPath(configJson as Record<string, unknown>, dotPath);
       if (typeof current === "string" && isUuidSecretRef(current)) {
-        refs.add(current);
+        addRef(current, dotPath);
       }
     }
     return refs;
@@ -107,7 +112,7 @@ export function extractSecretRefsFromConfig(
   // instanceConfigSchema.
   function walkAll(value: unknown): void {
     if (typeof value === "string") {
-      if (isUuidSecretRef(value)) refs.add(value);
+      if (isUuidSecretRef(value)) addRef(value, "$");
     } else if (Array.isArray(value)) {
       for (const item of value) walkAll(item);
     } else if (value !== null && typeof value === "object") {
@@ -207,11 +212,12 @@ export function createPluginSecretsHandler(
 ): PluginSecretsService {
   const { db, pluginId } = options;
   const registry = pluginRegistryService(db);
+  const secrets = secretService(db);
 
   // Rate limit: max 30 resolution attempts per plugin per minute
   const rateLimiter = createRateLimiter(30, 60_000);
 
-  let cachedAllowedRefs: Set<string> | null = null;
+  let cachedAllowedRefs: Map<string, Set<string>> | null = null;
   let cachedAllowedRefsExpiry = 0;
   const CONFIG_CACHE_TTL_MS = 30_000; // 30 seconds, matches event bus TTL
 
@@ -257,11 +263,12 @@ export function createPluginSecretsHandler(
 
         const schema = (plugin?.manifestJson as unknown as Record<string, unknown> | null)
           ?.instanceConfigSchema as Record<string, unknown> | undefined;
-        cachedAllowedRefs = extractSecretRefsFromConfig(configRow?.configJson, schema);
+        cachedAllowedRefs = extractSecretRefPathsFromConfig(configRow?.configJson, schema);
         cachedAllowedRefsExpiry = now + CONFIG_CACHE_TTL_MS;
       }
 
-      if (!cachedAllowedRefs.has(trimmedRef)) {
+      const allowedPaths = cachedAllowedRefs.get(trimmedRef);
+      if (!allowedPaths) {
         // Return "not found" to avoid leaking whether the secret exists
         throw secretNotFound(trimmedRef);
       }
@@ -279,34 +286,14 @@ export function createPluginSecretsHandler(
         throw secretNotFound(trimmedRef);
       }
 
-      // ---------------------------------------------------------------
-      // 3. Fetch the latest version's material
-      // ---------------------------------------------------------------
-      const versionRow = await db
-        .select()
-        .from(companySecretVersions)
-        .where(
-          and(
-            eq(companySecretVersions.secretId, secret.id),
-            eq(companySecretVersions.version, secret.latestVersion),
-          ),
-        )
-        .then((rows) => rows[0] ?? null);
-
-      if (!versionRow) {
-        throw secretVersionNotFound(trimmedRef);
-      }
-
-      // ---------------------------------------------------------------
-      // 4. Resolve through the appropriate secret provider
-      // ---------------------------------------------------------------
-      const provider = getSecretProvider(secret.provider as SecretProvider);
-      const resolved = await provider.resolveVersion({
-        material: versionRow.material as Record<string, unknown>,
-        externalRef: secret.externalRef,
+      return await secrets.resolveSecretValue(secret.companyId, secret.id, "latest", {
+        consumerType: "plugin",
+        consumerId: pluginId,
+        actorType: "plugin",
+        actorId: pluginId,
+        pluginId,
+        configPath: [...allowedPaths][0] ?? "$",
       });
-
-      return resolved;
     },
   };
 }
diff --git a/server/src/services/routines.ts b/server/src/services/routines.ts
index 14f244155a2..d40d62a8c23 100644
--- a/server/src/services/routines.ts
+++ b/server/src/services/routines.ts
@@ -3,6 +3,7 @@ import { and, asc, desc, eq, inArray, isNotNull, isNull, lte, ne, not, or, sql }
 import type { Db } from "@paperclipai/db";
 import {
   agents,
+  companySecretBindings,
   companySecretVersions,
   companySecrets,
   executionWorkspaces,
@@ -957,9 +958,15 @@ export function routineService(
       description: `Webhook auth for routine ${routineId}`,
     };
     const provider = getSecretProvider(input.provider);
-    const prepared = await provider.createVersion({
+    const prepared = await provider.createSecret({
       value: input.value,
       externalRef: null,
+      context: {
+        companyId,
+        secretKey: input.name,
+        secretName: input.name,
+        version: 1,
+      },
     });
 
     const insertSecret = async (secretDb: Db) => {
@@ -967,11 +974,16 @@ export function routineService(
         .insert(companySecrets)
         .values({
           companyId,
+          key: input.name,
           name: input.name,
           provider: input.provider,
+          status: "active",
+          managedMode: "paperclip_managed",
           externalRef: prepared.externalRef,
+          providerMetadata: null,
           latestVersion: 1,
           description: input.description,
+          lastRotatedAt: new Date(),
           createdByAgentId: actor.agentId ?? null,
           createdByUserId: actor.userId ?? null,
         })
@@ -983,10 +995,21 @@ export function routineService(
         version: 1,
         material: prepared.material,
         valueSha256: prepared.valueSha256,
+        fingerprintSha256: prepared.fingerprintSha256 ?? prepared.valueSha256,
+        providerVersionRef: prepared.providerVersionRef ?? null,
+        status: "current",
         createdByAgentId: actor.agentId ?? null,
         createdByUserId: actor.userId ?? null,
       });
 
+      await secretDb.insert(companySecretBindings).values({
+        companyId,
+        secretId: secret.id,
+        targetType: "routine",
+        targetId: routineId,
+        configPath: "webhookSecret",
+      });
+
       return secret;
     };
 
@@ -1004,7 +1027,13 @@ export function routineService(
       .where(eq(companySecrets.id, trigger.secretId))
       .then((rows) => rows[0] ?? null);
     if (!secret || secret.companyId !== companyId) throw notFound("Routine trigger secret not found");
-    const value = await secretsSvc.resolveSecretValue(companyId, trigger.secretId, "latest");
+    const value = await secretsSvc.resolveSecretValue(companyId, trigger.secretId, "latest", {
+      consumerType: "routine",
+      consumerId: trigger.routineId,
+      actorType: "system",
+      actorId: null,
+      configPath: "webhookSecret",
+    });
     return value;
   }
 
diff --git a/server/src/services/secrets.ts b/server/src/services/secrets.ts
index 7af1cf8f36f..4ff2d00e629 100644
--- a/server/src/services/secrets.ts
+++ b/server/src/services/secrets.ts
@@ -41,6 +41,22 @@ type SecretConsumerContext = {
   pluginId?: string | null;
 };
 
+export type RuntimeSecretManifestEntry = {
+  configPath: string;
+  envKey: string | null;
+  secretId: string;
+  secretKey: string;
+  version: number;
+  provider: SecretProvider;
+  outcome: "success" | "failure";
+  errorCode?: string | null;
+};
+
+type RuntimeSecretResolution = {
+  value: string;
+  manifestEntry: RuntimeSecretManifestEntry;
+};
+
 function asRecord(value: unknown): Record<string, unknown> | null {
   if (typeof value !== "object" || value === null || Array.isArray(value)) return null;
   return value as Record<string, unknown>;
@@ -188,15 +204,16 @@ export function secretService(db: Db) {
     return secret;
   }
 
-  async function resolveSecretValue(
+  async function resolveSecretValueInternal(
     companyId: string,
     secretId: string,
     version: number | "latest",
     context?: SecretConsumerContext,
-  ): Promise<string> {
+  ): Promise<RuntimeSecretResolution> {
     const secret = await assertSecretInCompany(companyId, secretId);
     const resolvedVersion = version === "latest" ? secret.latestVersion : version;
     const providerId = secret.provider as SecretProvider;
+    const configPath = context?.configPath ?? null;
     try {
       if (secret.status !== "active") {
         throw unprocessable("Secret is not active");
@@ -233,8 +250,20 @@ export function secretService(db: Db) {
           outcome: "success",
         }),
       ]);
-      return value;
+      return {
+        value,
+        manifestEntry: {
+          configPath: configPath ?? "",
+          envKey: configPath?.startsWith("env.") ? configPath.slice("env.".length) : null,
+          secretId: secret.id,
+          secretKey: secret.key,
+          version: resolvedVersion,
+          provider: providerId,
+          outcome: "success",
+        },
+      };
     } catch (err) {
+      const errorCode = err instanceof Error ? err.message.slice(0, 120) : "resolution_failed";
       await recordAccessEvent({
         companyId,
         secretId: secret.id,
@@ -242,12 +271,21 @@ export function secretService(db: Db) {
         provider: providerId,
         context,
         outcome: "failure",
-        errorCode: err instanceof Error ? err.message.slice(0, 120) : "resolution_failed",
+        errorCode,
       });
       throw err;
     }
   }
 
+  async function resolveSecretValue(
+    companyId: string,
+    secretId: string,
+    version: number | "latest",
+    context?: SecretConsumerContext,
+  ): Promise<string> {
+    return (await resolveSecretValueInternal(companyId, secretId, version, context)).value;
+  }
+
   async function normalizeEnvConfig(
     companyId: string,
     envValue: unknown,
@@ -607,6 +645,62 @@ export function secretService(db: Db) {
         .then((rows) => rows[0]);
     },
 
+    syncSecretRefsForTarget: async (
+      companyId: string,
+      target: { targetType: SecretBindingTargetType; targetId: string },
+      refs: Array<{
+        secretId: string;
+        configPath: string;
+        versionSelector?: SecretVersionSelector;
+        required?: boolean;
+        label?: string | null;
+      }>,
+    ) => {
+      const normalizedRefs: Array<{
+        secretId: string;
+        configPath: string;
+        versionSelector: SecretVersionSelector;
+        required: boolean;
+        label: string | null;
+      }> = [];
+      for (const ref of refs) {
+        await assertSecretInCompany(companyId, ref.secretId);
+        normalizedRefs.push({
+          secretId: ref.secretId,
+          configPath: ref.configPath,
+          versionSelector: ref.versionSelector ?? "latest",
+          required: ref.required ?? true,
+          label: ref.label ?? null,
+        });
+      }
+
+      await db.transaction(async (tx) => {
+        await tx
+          .delete(companySecretBindings)
+          .where(
+            and(
+              eq(companySecretBindings.companyId, companyId),
+              eq(companySecretBindings.targetType, target.targetType),
+              eq(companySecretBindings.targetId, target.targetId),
+            ),
+          );
+        if (normalizedRefs.length === 0) return;
+        await tx.insert(companySecretBindings).values(
+          normalizedRefs.map((ref) => ({
+            companyId,
+            secretId: ref.secretId,
+            targetType: target.targetType,
+            targetId: target.targetId,
+            configPath: ref.configPath,
+            versionSelector: String(ref.versionSelector),
+            required: ref.required,
+            label: ref.label,
+          })),
+        );
+      });
+      return normalizedRefs;
+    },
+
     syncEnvBindingsForTarget: async (
       companyId: string,
       target: { targetType: SecretBindingTargetType; targetId: string; pathPrefix?: string },
@@ -711,11 +805,12 @@ export function secretService(db: Db) {
       companyId: string,
       envValue: unknown,
       context?: Omit<SecretConsumerContext, "configPath">,
-    ): Promise<{ env: Record<string, string>; secretKeys: Set<string> }> => {
+    ): Promise<{ env: Record<string, string>; secretKeys: Set<string>; manifest: RuntimeSecretManifestEntry[] }> => {
       const record = asRecord(envValue);
-      if (!record) return { env: {} as Record<string, string>, secretKeys: new Set<string>() };
+      if (!record) return { env: {} as Record<string, string>, secretKeys: new Set<string>(), manifest: [] };
       const resolved: Record<string, string> = {};
       const secretKeys = new Set<string>();
+      const manifest: RuntimeSecretManifestEntry[] = [];
 
       for (const [key, rawBinding] of Object.entries(record)) {
         if (!ENV_KEY_RE.test(key)) {
@@ -729,32 +824,35 @@ export function secretService(db: Db) {
         if (binding.type === "plain") {
           resolved[key] = binding.value;
         } else {
-          resolved[key] = await resolveSecretValue(
+          const secretResolution = await resolveSecretValueInternal(
             companyId,
             binding.secretId,
             binding.version,
             context ? { ...context, configPath: `env.${key}` } : undefined,
           );
+          resolved[key] = secretResolution.value;
+          manifest.push(secretResolution.manifestEntry);
           secretKeys.add(key);
         }
       }
-      return { env: resolved, secretKeys };
+      return { env: resolved, secretKeys, manifest };
     },
 
     resolveAdapterConfigForRuntime: async (
       companyId: string,
       adapterConfig: Record<string, unknown>,
       context?: Omit<SecretConsumerContext, "configPath">,
-    ): Promise<{ config: Record<string, unknown>; secretKeys: Set<string> }> => {
+    ): Promise<{ config: Record<string, unknown>; secretKeys: Set<string>; manifest: RuntimeSecretManifestEntry[] }> => {
       const resolved = { ...adapterConfig };
       const secretKeys = new Set<string>();
+      const manifest: RuntimeSecretManifestEntry[] = [];
       if (!Object.prototype.hasOwnProperty.call(adapterConfig, "env")) {
-        return { config: resolved, secretKeys };
+        return { config: resolved, secretKeys, manifest };
       }
       const record = asRecord(adapterConfig.env);
       if (!record) {
         resolved.env = {};
-        return { config: resolved, secretKeys };
+        return { config: resolved, secretKeys, manifest };
       }
       const env: Record<string, string> = {};
       for (const [key, rawBinding] of Object.entries(record)) {
@@ -769,17 +867,19 @@ export function secretService(db: Db) {
         if (binding.type === "plain") {
           env[key] = binding.value;
         } else {
-          env[key] = await resolveSecretValue(
+          const secretResolution = await resolveSecretValueInternal(
             companyId,
             binding.secretId,
             binding.version,
             context ? { ...context, configPath: `env.${key}` } : undefined,
           );
+          env[key] = secretResolution.value;
+          manifest.push(secretResolution.manifestEntry);
           secretKeys.add(key);
         }
       }
       resolved.env = env;
-      return { config: resolved, secretKeys };
+      return { config: resolved, secretKeys, manifest };
     },
   };
 }