diff --git a/doc/DATABASE.md b/doc/DATABASE.md
index 18a7208f208..e4407d2e17d 100644
--- a/doc/DATABASE.md
+++ b/doc/DATABASE.md
@@ -202,6 +202,17 @@ Triage writes serialize on the company and attention-source identity so concurre
 
 The plugin runtime tracks plugin-owned database namespaces and migrations in `plugin_database_namespaces` and `plugin_migrations`. Hosted deployments that separate runtime and migration connections should set `DATABASE_MIGRATION_URL`; plugin namespace migration work uses the migration connection when present.
 
+## Agent instruction bundle durability
+
+Managed agent instruction bundles are stored in Postgres through `built_in_managed_resources` instruction bindings; the instance `companies/<company-id>/agents/<agent-id>/instructions/` directory is a rebuildable materialization cache. Existing installations can import disk-backed managed bundles idempotently with:
+
+```sh
+pnpm instructions:import-bindings          # report only
+pnpm instructions:import-bindings --apply  # persist missing bindings
+```
+
+Bundles explicitly configured with `instructionsBundleMode: "external"` remain pointers by design. Their roots genuinely live outside Paperclip's managed instance tree, are not copied into Postgres, and must be backed up by the external owner.
+
 ## Backups
 
 Paperclip supports automatic and manual logical database backups. These dumps include
diff --git a/package.json b/package.json
index 7ef3cad63f1..0919049f07a 100644
--- a/package.json
+++ b/package.json
@@ -66,7 +66,8 @@
     "test:release-smoke:headed": "npx playwright test --config tests/release-smoke/playwright.config.ts --headed",
     "metrics:paperclip-commits": "tsx scripts/paperclip-commit-metrics.ts",
     "perf:issue-chat-long-thread": "node scripts/measure-issue-chat-long-thread.mjs",
-    "connections:ingest-app-definitions": "node scripts/ingest-app-definitions.mjs"
+    "connections:ingest-app-definitions": "node scripts/ingest-app-definitions.mjs",
+    "instructions:import-bindings": "pnpm --filter @paperclipai/server exec tsx scripts/import-agent-instruction-bindings.ts"
   },
   "devDependencies": {
     "@playwright/test": "^1.61.1",
diff --git a/server/scripts/import-agent-instruction-bindings.ts b/server/scripts/import-agent-instruction-bindings.ts
new file mode 100644
index 00000000000..f62541449ee
--- /dev/null
+++ b/server/scripts/import-agent-instruction-bindings.ts
@@ -0,0 +1,54 @@
+import { and, eq } from "drizzle-orm";
+import { agents, builtInManagedResources, createDb } from "@paperclipai/db";
+import { resolveDatabaseTarget } from "../../packages/db/src/runtime-config.js";
+import { agentInstructionsService } from "../src/services/agent-instructions.js";
+
+function asRecord(value: unknown): Record<string, unknown> {
+  return typeof value === "object" && value !== null && !Array.isArray(value) ? value as Record<string, unknown> : {};
+}
+
+async function main() {
+  const target = resolveDatabaseTarget();
+  const dbUrl = target.mode === "postgres"
+    ? target.connectionString
+    : `postgres://paperclip:paperclip@127.0.0.1:${target.port}/paperclip`;
+  const apply = process.argv.includes("--apply");
+  const db = createDb(dbUrl);
+  const instructions = agentInstructionsService(db);
+  let imported = 0;
+  let skippedExternal = 0;
+  let skippedEmpty = 0;
+  let alreadyBound = 0;
+
+  for (const agent of await db.select().from(agents)) {
+    const config = asRecord(agent.adapterConfig);
+    if (config.instructionsBundleMode === "external") {
+      skippedExternal += 1;
+      continue;
+    }
+    const existing = await db.select({ id: builtInManagedResources.id }).from(builtInManagedResources).where(and(
+      eq(builtInManagedResources.companyId, agent.companyId),
+      eq(builtInManagedResources.resourceKind, "instructions"),
+      eq(builtInManagedResources.resourceId, agent.id),
+    )).then((rows) => rows[0] ?? null);
+    if (existing) {
+      alreadyBound += 1;
+      continue;
+    }
+    const bundle = await instructions.exportFiles(agent);
+    if (Object.keys(bundle.files).length === 0) {
+      skippedEmpty += 1;
+      continue;
+    }
+    if (apply) await instructions.persistManagedBundle(agent, bundle.entryFile, bundle.files);
+    imported += 1;
+  }
+
+  console.log(JSON.stringify({ mode: apply ? "apply" : "dry-run", imported, alreadyBound, skippedExternal, skippedEmpty }, null, 2));
+  process.exit(0);
+}
+
+void main().catch((error) => {
+  console.error(error);
+  process.exit(1);
+});
diff --git a/server/src/routes/agents.ts b/server/src/routes/agents.ts
index 7ff546cb9ff..7321c387d2e 100644
--- a/server/src/routes/agents.ts
+++ b/server/src/routes/agents.ts
@@ -386,7 +386,7 @@ export function agentRoutes(
   const recovery = recoveryService(db, { enqueueWakeup: heartbeat.wakeup });
   const issueApprovalsSvc = issueApprovalService(db);
   const secretsSvc = secretService(db);
-  const instructions = agentInstructionsService();
+  const instructions = agentInstructionsService(db);
   const companySkills = companySkillService(db);
   const workspaceOperations = workspaceOperationService(db);
   const instanceSettings = instanceSettingsService(db);
diff --git a/server/src/services/agent-instructions.ts b/server/src/services/agent-instructions.ts
index 6dcbb38f047..81b9a80abf5 100644
--- a/server/src/services/agent-instructions.ts
+++ b/server/src/services/agent-instructions.ts
@@ -1,5 +1,9 @@
 import fs from "node:fs/promises";
 import path from "node:path";
+import { createHash } from "node:crypto";
+import { and, eq } from "drizzle-orm";
+import type { Db } from "@paperclipai/db";
+import { builtInManagedResources } from "@paperclipai/db";
 import { notFound, unprocessable } from "../errors.js";
 import { resolveHomeAwarePath, resolvePaperclipInstanceRoot } from "../home-paths.js";
 
@@ -451,9 +455,69 @@ export function syncInstructionsBundleConfigFromFilePath(
   return applyBundleConfig(next, { mode, rootPath, entryFile });
 }
 
-export function agentInstructionsService() {
+export function agentInstructionsService(db?: Db) {
+  async function getStoredBundle(agent: AgentLike) {
+    if (!db) return null;
+    const rows = await db.select().from(builtInManagedResources).where(and(
+      eq(builtInManagedResources.companyId, agent.companyId),
+      eq(builtInManagedResources.resourceKind, "instructions"),
+      eq(builtInManagedResources.resourceId, agent.id),
+    ));
+    for (const row of rows) {
+      const defaults = asRecord(row.defaultsJson);
+      const files = Object.fromEntries(Object.entries(asRecord(defaults.files)).filter((entry): entry is [string, string] => typeof entry[1] === "string"));
+      if (Object.keys(files).length > 0) return { row, entryFile: asString(defaults.entryFile) ?? ENTRY_FILE_DEFAULT, files };
+    }
+    return null;
+  }
+
+  async function persistManagedBundle(agent: AgentLike, entryFile: string, files: Record<string, string>) {
+    if (!db || Object.keys(files).length === 0) return;
+    const existing = await getStoredBundle(agent);
+    const stockHash = `sha256:${createHash("sha256").update(JSON.stringify({ entryFile, files })).digest("hex")}`;
+    const values = {
+      companyId: agent.companyId,
+      bundleKey: existing?.row.bundleKey ?? `custom-agent:${agent.id}`,
+      resourceKind: "instructions",
+      resourceKey: existing?.row.resourceKey ?? "bundle",
+      resourceId: agent.id,
+      stockVersion: existing?.row.stockVersion ?? "custom-v1",
+      stockHash,
+      defaultsJson: { entryFile, files },
+    };
+    await db.insert(builtInManagedResources).values(values).onConflictDoUpdate({
+      target: [builtInManagedResources.companyId, builtInManagedResources.bundleKey, builtInManagedResources.resourceKind, builtInManagedResources.resourceKey],
+      set: { resourceId: agent.id, stockHash, defaultsJson: values.defaultsJson, updatedAt: new Date() },
+    });
+  }
+
+  async function resolveState(agent: AgentLike) {
+    const derived = deriveBundleState(agent);
+    if (derived.mode !== "external") {
+      const stored = await getStoredBundle(agent);
+      if (stored) {
+        const rootPath = resolveManagedInstructionsRoot(agent);
+        const stat = await statIfExists(rootPath);
+        const files = stat?.isDirectory() ? await listFilesRecursive(rootPath) : [];
+        if (files.length === 0) {
+          await fs.mkdir(rootPath, { recursive: true });
+          await writeBundleFiles(rootPath, stored.files, { overwriteExisting: true });
+        }
+        return recoverManagedBundleState(agent, { ...derived, mode: "managed", rootPath, entryFile: stored.entryFile, resolvedEntryPath: path.resolve(rootPath, stored.entryFile) });
+      }
+    }
+    return recoverManagedBundleState(agent, derived);
+  }
+
+  async function persistState(agent: AgentLike, state: BundleState) {
+    if (state.mode !== "managed" || !state.rootPath) return;
+    const relativePaths = await listFilesRecursive(state.rootPath);
+    const files = Object.fromEntries(await Promise.all(relativePaths.map(async (relativePath) => [relativePath, await fs.readFile(resolvePathWithinRoot(state.rootPath!, relativePath), "utf8")] as const)));
+    await persistManagedBundle(agent, state.entryFile, files);
+  }
+
   async function getBundle(agent: AgentLike): Promise<AgentInstructionsBundle> {
-    const state = await recoverManagedBundleState(agent, deriveBundleState(agent));
+    const state = await resolveState(agent);
     if (!state.rootPath) return toBundle(agent, state, []);
     const stat = await statIfExists(state.rootPath);
     if (!stat?.isDirectory()) {
@@ -468,7 +532,7 @@ export function agentInstructionsService() {
   }
 
   async function readFile(agent: AgentLike, relativePath: string): Promise<AgentInstructionsFileDetail> {
-    const state = await recoverManagedBundleState(agent, deriveBundleState(agent));
+    const state = await resolveState(agent);
     if (relativePath === LEGACY_PROMPT_TEMPLATE_PATH) {
       const content = asString(state.config[PROMPT_KEY]);
       if (content === null) throw notFound("Instructions file not found");
@@ -510,7 +574,7 @@ export function agentInstructionsService() {
     options?: { clearLegacyPromptTemplate?: boolean },
   ): Promise<{ adapterConfig: Record<string, unknown>; state: BundleState }> {
     const derived = deriveBundleState(agent);
-    const current = await recoverManagedBundleState(agent, derived);
+    const current = await resolveState(agent);
     if (current.rootPath && current.mode) {
       const adapterConfig = buildPersistedBundleConfig(derived, current, options);
       return {
@@ -554,7 +618,7 @@ export function agentInstructionsService() {
       clearLegacyPromptTemplate?: boolean;
     },
   ): Promise<{ bundle: AgentInstructionsBundle; adapterConfig: Record<string, unknown> }> {
-    const state = await recoverManagedBundleState(agent, deriveBundleState(agent));
+    const state = await resolveState(agent);
     const nextMode = input.mode ?? state.mode ?? "managed";
     const nextEntryFile = input.entryFile ? normalizeRelativeFilePath(input.entryFile) : state.entryFile;
     let nextRootPath: string;
@@ -592,7 +656,9 @@ export function agentInstructionsService() {
       entryFile: nextEntryFile,
       clearLegacyPromptTemplate: input.clearLegacyPromptTemplate,
     });
-    const nextBundle = await getBundle({ ...agent, adapterConfig: nextConfig });
+    const nextAgent = { ...agent, adapterConfig: nextConfig };
+    if (nextMode === "managed") await persistState(nextAgent, await resolveState(nextAgent));
+    const nextBundle = await getBundle(nextAgent);
     return { bundle: nextBundle, adapterConfig: nextConfig };
   }
 
@@ -625,6 +691,7 @@ export function agentInstructionsService() {
     await fs.mkdir(path.dirname(absolutePath), { recursive: true });
     await fs.writeFile(absolutePath, content, "utf8");
     const nextAgent = { ...agent, adapterConfig: prepared.adapterConfig };
+    await persistState(nextAgent, prepared.state);
     const [bundle, file] = await Promise.all([
       getBundle(nextAgent),
       readFile(nextAgent, relativePath),
@@ -637,7 +704,7 @@ export function agentInstructionsService() {
     adapterConfig: Record<string, unknown>;
   }> {
     const derived = deriveBundleState(agent);
-    const state = await recoverManagedBundleState(agent, derived);
+    const state = await resolveState(agent);
     if (relativePath === LEGACY_PROMPT_TEMPLATE_PATH) {
       throw unprocessable("Cannot delete the legacy promptTemplate pseudo-file");
     }
@@ -649,6 +716,7 @@ export function agentInstructionsService() {
     const absolutePath = resolvePathWithinRoot(state.rootPath, normalizedPath);
     await fs.rm(absolutePath, { force: true });
     const adapterConfig = buildPersistedBundleConfig(derived, state);
+    await persistState({ ...agent, adapterConfig }, state);
     const bundle = await getBundle({ ...agent, adapterConfig });
     return { bundle, adapterConfig };
   }
@@ -658,7 +726,7 @@ export function agentInstructionsService() {
     entryFile: string;
     warnings: string[];
   }> {
-    const state = await recoverManagedBundleState(agent, deriveBundleState(agent));
+    const state = await resolveState(agent);
     if (state.rootPath) {
       const stat = await statIfExists(state.rootPath);
       if (stat?.isDirectory()) {
@@ -718,7 +786,11 @@ export function agentInstructionsService() {
       entryFile,
       clearLegacyPromptTemplate: options?.clearLegacyPromptTemplate,
     });
-    const bundle = await getBundle({ ...agent, adapterConfig });
+    const nextAgent = { ...agent, adapterConfig };
+    const persistedFiles = Object.fromEntries(normalizedEntries);
+    if (!(entryFile in persistedFiles)) persistedFiles[entryFile] = "";
+    await persistManagedBundle(nextAgent, entryFile, persistedFiles);
+    const bundle = await getBundle(nextAgent);
     return { bundle, adapterConfig };
   }
 
@@ -731,5 +803,6 @@ export function agentInstructionsService() {
     exportFiles,
     ensureManagedBundle: ensureWritableBundle,
     materializeManagedBundle,
+    persistManagedBundle,
   };
 }
diff --git a/server/src/services/company-portability.ts b/server/src/services/company-portability.ts
index c86c2bbbefd..8d8dcb8a8ce 100644
--- a/server/src/services/company-portability.ts
+++ b/server/src/services/company-portability.ts
@@ -3476,7 +3476,7 @@ export function companyPortabilityService(db: Db, storage?: StorageService) {
   const companies = companyService(db);
   const agents = agentService(db);
   const assetRecords = assetService(db);
-  const instructions = agentInstructionsService();
+  const instructions = agentInstructionsService(db);
   const access = accessService(db);
   const projects = projectService(db);
   const issues = issueService(db);
diff --git a/server/src/services/plugin-managed-agents.ts b/server/src/services/plugin-managed-agents.ts
index ea95b59ce8c..07f292aa3c2 100644
--- a/server/src/services/plugin-managed-agents.ts
+++ b/server/src/services/plugin-managed-agents.ts
@@ -176,7 +176,7 @@ export function pluginManagedAgentService(
 ) {
   const agentSvc = agentService(db);
   const approvalSvc = approvalService(db);
-  const instructions = agentInstructionsService();
+  const instructions = agentInstructionsService(db);
 
   function declarationFor(agentKey: string) {
     const declaration = options.manifest?.agents?.find((agent) => agent.agentKey === agentKey);