diff --git a/server/src/__tests__/access-routes-permissions-upgrade.test.ts b/server/src/__tests__/access-routes-permissions-upgrade.test.ts
new file mode 100644
index 00000000000..9db328d4519
--- /dev/null
+++ b/server/src/__tests__/access-routes-permissions-upgrade.test.ts
@@ -0,0 +1,167 @@
+import { randomUUID } from "node:crypto";
+import express from "express";
+import request from "supertest";
+import { and, eq } from "drizzle-orm";
+import { afterAll, afterEach, beforeAll, describe, expect, it, vi } from "vitest";
+import {
+  activityLog,
+  companies,
+  companyMemberships,
+  createDb,
+  principalPermissionGrants,
+} from "@paperclipai/db";
+import {
+  getEmbeddedPostgresTestSupport,
+  startEmbeddedPostgresTestDatabase,
+} from "./helpers/embedded-postgres.js";
+
+vi.hoisted(() => {
+  process.env.PAPERCLIP_HOME = "/tmp/paperclip-test-home";
+  process.env.PAPERCLIP_INSTANCE_ID = "vitest";
+  process.env.PAPERCLIP_LOG_DIR = "/tmp/paperclip-test-home/logs";
+  process.env.PAPERCLIP_IN_WORKTREE = "false";
+});
+
+const embeddedPostgresSupport = await getEmbeddedPostgresTestSupport();
+const describeEmbeddedPostgres = embeddedPostgresSupport.supported ? describe : describe.skip;
+
+type Db = ReturnType<typeof createDb>;
+
+async function createApp(db: Db, companyId: string, userId: string) {
+  process.env.PAPERCLIP_LOG_DIR = "/tmp/paperclip-test-home/logs";
+  process.env.PAPERCLIP_IN_WORKTREE = "false";
+  const { accessRoutes } = await import("../routes/access.js");
+  const app = express();
+  app.use(express.json());
+  app.use((req, _res, next) => {
+    req.actor = {
+      type: "board",
+      userId,
+      source: "local_implicit",
+      companyIds: [companyId],
+      memberships: [{ companyId, membershipRole: "owner", status: "active" }],
+      isInstanceAdmin: true,
+    };
+    next();
+  });
+  app.use("/api", accessRoutes(db, {
+    deploymentMode: "authenticated",
+    deploymentExposure: "private",
+    bindHost: "127.0.0.1",
+    allowedHostnames: [],
+  }));
+  app.use((err: any, _req: express.Request, res: express.Response, _next: express.NextFunction) => {
+    res.status(err.status ?? 500).json({ error: err.message ?? "Internal server error" });
+  });
+  return app;
+}
+
+async function createCompanyWithOwner(db: Db) {
+  const company = await db
+    .insert(companies)
+    .values({
+      name: `Access Routes ${randomUUID()}`,
+      issuePrefix: `AR${randomUUID().replace(/-/g, "").slice(0, 6).toUpperCase()}`,
+    })
+    .returning()
+    .then((rows) => rows[0]!);
+  const owner = await db
+    .insert(companyMemberships)
+    .values({
+      companyId: company.id,
+      principalType: "user",
+      principalId: `owner-${randomUUID()}`,
+      status: "active",
+      membershipRole: "owner",
+    })
+    .returning()
+    .then((rows) => rows[0]!);
+  return { company, owner };
+}
+
+describeEmbeddedPostgres("access routes permissions upgrade compatibility", () => {
+  let db!: Db;
+  let tempDb: Awaited<ReturnType<typeof startEmbeddedPostgresTestDatabase>> | null = null;
+
+  beforeAll(async () => {
+    tempDb = await startEmbeddedPostgresTestDatabase("paperclip-access-routes-permissions-upgrade-");
+    db = createDb(tempDb.connectionString);
+  }, 20_000);
+
+  afterEach(async () => {
+    await db.delete(activityLog);
+    await db.delete(principalPermissionGrants);
+    await db.delete(companyMemberships);
+    await db.delete(companies);
+  });
+
+  afterAll(async () => {
+    await tempDb?.cleanup();
+  });
+
+  it("rejects owner self-lockout through the member route after the permissions upgrade", async () => {
+    const { company, owner } = await createCompanyWithOwner(db);
+
+    const res = await request(await createApp(db, company.id, owner.principalId))
+      .patch(`/api/companies/${company.id}/members/${owner.id}`)
+      .send({ membershipRole: "admin" });
+
+    expect(res.status, JSON.stringify(res.body)).toBe(403);
+    expect(res.body.error).toContain("You cannot remove yourself");
+
+    const unchanged = await db
+      .select()
+      .from(companyMemberships)
+      .where(eq(companyMemberships.id, owner.id))
+      .then((rows) => rows[0]!);
+    expect(unchanged.membershipRole).toBe("owner");
+  });
+
+  it("keeps custom grants when the role-only member route changes a member role", async () => {
+    const { company, owner } = await createCompanyWithOwner(db);
+    const member = await db
+      .insert(companyMemberships)
+      .values({
+        companyId: company.id,
+        principalType: "user",
+        principalId: `admin-${randomUUID()}`,
+        status: "active",
+        membershipRole: "admin",
+      })
+      .returning()
+      .then((rows) => rows[0]!);
+    const customScope = { projectIds: ["project-1"] };
+    await db.insert(principalPermissionGrants).values({
+      companyId: company.id,
+      principalType: "user",
+      principalId: member.principalId,
+      permissionKey: "tasks:assign_scope",
+      scope: customScope,
+      grantedByUserId: owner.principalId,
+    });
+
+    const res = await request(await createApp(db, company.id, owner.principalId))
+      .patch(`/api/companies/${company.id}/members/${member.id}`)
+      .send({ membershipRole: "operator" });
+
+    expect(res.status, JSON.stringify(res.body)).toBe(200);
+    expect(res.body.membershipRole).toBe("operator");
+
+    const grants = await db
+      .select()
+      .from(principalPermissionGrants)
+      .where(
+        and(
+          eq(principalPermissionGrants.companyId, company.id),
+          eq(principalPermissionGrants.principalType, "user"),
+          eq(principalPermissionGrants.principalId, member.principalId),
+        ),
+      );
+    expect(grants).toHaveLength(1);
+    expect(grants[0]).toMatchObject({
+      permissionKey: "tasks:assign_scope",
+      scope: customScope,
+      grantedByUserId: owner.principalId,
+    });
+  });
+});
diff --git a/server/src/__tests__/permissions-upgrade-boundary-routes.test.ts b/server/src/__tests__/permissions-upgrade-boundary-routes.test.ts
new file mode 100644
index 00000000000..2d53659115a
--- /dev/null
+++ b/server/src/__tests__/permissions-upgrade-boundary-routes.test.ts
@@ -0,0 +1,348 @@
+import { randomUUID } from "node:crypto";
+import express from "express";
+import request from "supertest";
+import { afterAll, afterEach, beforeAll, describe, expect, it, vi } from "vitest";
+import {
+  activityLog,
+  agents,
+  assets,
+  companies,
+  companyMemberships,
+  createDb,
+  documents,
+  heartbeatRuns,
+  issueAttachments,
+  issueComments,
+  issueDocuments,
+  issues,
+  issueWorkProducts,
+  principalPermissionGrants,
+} from "@paperclipai/db";
+import {
+  getEmbeddedPostgresTestSupport,
+  startEmbeddedPostgresTestDatabase,
+} from "./helpers/embedded-postgres.js";
+
+vi.hoisted(() => {
+  process.env.PAPERCLIP_HOME = "/tmp/paperclip-test-home";
+  process.env.PAPERCLIP_INSTANCE_ID = "vitest";
+  process.env.PAPERCLIP_LOG_DIR = "/tmp/paperclip-test-home/logs";
+  process.env.PAPERCLIP_IN_WORKTREE = "false";
+});
+
+vi.mock("../services/issue-assignment-wakeup.js", () => ({
+  queueIssueAssignmentWakeup: vi.fn(),
+}));
+
+const embeddedPostgresSupport = await getEmbeddedPostgresTestSupport();
+const describeEmbeddedPostgres = embeddedPostgresSupport.supported ? describe : describe.skip;
+
+type Db = ReturnType<typeof createDb>;
+
+function agentActor(companyId: string, agentId: string): Express.Request["actor"] {
+  return {
+    type: "agent",
+    agentId,
+    companyId,
+    runId: null,
+    source: "agent_jwt",
+  };
+}
+
+async function createApp(db: Db, actor: Express.Request["actor"]) {
+  process.env.PAPERCLIP_LOG_DIR = "/tmp/paperclip-test-home/logs";
+  process.env.PAPERCLIP_IN_WORKTREE = "false";
+  const [{ activityRoutes }, { issueRoutes }] = await Promise.all([
+    import("../routes/activity.js"),
+    import("../routes/issues.js"),
+  ]);
+  const app = express();
+  app.use(express.json());
+  app.use((req, _res, next) => {
+    req.actor = actor;
+    next();
+  });
+  app.use("/api", issueRoutes(db, {} as any));
+  app.use("/api", activityRoutes(db));
+  app.use((err: any, _req: express.Request, res: express.Response, _next: express.NextFunction) => {
+    res.status(err.status ?? 500).json({ error: err.message ?? "Internal server error" });
+  });
+  return app;
+}
+
+async function seedCompany(db: Db, label: string) {
+  return db
+    .insert(companies)
+    .values({
+      name: `Permissions Boundary ${label}`,
+      issuePrefix: `PB${randomUUID().replace(/-/g, "").slice(0, 6).toUpperCase()}`,
+    })
+    .returning()
+    .then((rows) => rows[0]!);
+}
+
+async function seedAgent(
+  db: Db,
+  companyId: string,
+  input: { role?: string; permissions?: Record<string, unknown>; status?: "active" | "idle" } = {},
+) {
+  return db
+    .insert(agents)
+    .values({
+      companyId,
+      name: `Agent ${randomUUID()}`,
+      role: input.role ?? "engineer",
+      status: input.status ?? "active",
+      adapterType: "process",
+      adapterConfig: {},
+      runtimeConfig: {},
+      permissions: input.permissions ?? {},
+    })
+    .returning()
+    .then((rows) => rows[0]!);
+}
+
+describeEmbeddedPostgres("permissions upgrade visibility and route boundaries", () => {
+  let db!: Db;
+  let tempDb: Awaited<ReturnType<typeof startEmbeddedPostgresTestDatabase>> | null = null;
+
+  beforeAll(async () => {
+    tempDb = await startEmbeddedPostgresTestDatabase("paperclip-permissions-boundary-routes-");
+    db = createDb(tempDb.connectionString);
+  }, 20_000);
+
+  afterEach(async () => {
+    await db.delete(issueAttachments);
+    await db.delete(assets);
+    await db.delete(issueDocuments);
+    await db.delete(documents);
+    await db.delete(issueWorkProducts);
+    await db.delete(issueComments);
+    await db.delete(activityLog);
+    await db.delete(principalPermissionGrants);
+    await db.delete(companyMemberships);
+    await db.delete(heartbeatRuns);
+    await db.delete(issues);
+    await db.delete(agents);
+    await db.delete(companies);
+  });
+
+  afterAll(async () => {
+    await tempDb?.cleanup();
+  });
+
+  it("keeps V1 private agent visibility from becoming issue, comment, document, attachment, activity, or work product privacy", async () => {
+    const company = await seedCompany(db, "Visibility");
+    const readerAgent = await seedAgent(db, company.id);
+    const privateTargetAgent = await seedAgent(db, company.id, {
+      permissions: {
+        authorizationPolicy: {
+          agentVisibility: {
+            mode: "private",
+            hiddenFromDefaultDirectory: true,
+          },
+          assignmentPolicy: { mode: "protected" },
+          protectedAgent: { requiresApproval: false },
+          managedBy: "permissions-extension",
+        },
+      },
+    });
+    const issue = await db
+      .insert(issues)
+      .values({
+        companyId: company.id,
+        identifier: `${company.issuePrefix}-1`,
+        title: "Visible work for a private target agent",
+        status: "todo",
+        priority: "medium",
+        assigneeAgentId: privateTargetAgent.id,
+      })
+      .returning()
+      .then((rows) => rows[0]!);
+    const comment = await db
+      .insert(issueComments)
+      .values({
+        companyId: company.id,
+        issueId: issue.id,
+        authorAgentId: privateTargetAgent.id,
+        body: "Private target agent status is still company-visible.",
+      })
+      .returning()
+      .then((rows) => rows[0]!);
+    const doc = await db
+      .insert(documents)
+      .values({
+        companyId: company.id,
+        title: "Plan",
+        latestBody: "Shared plan body",
+        createdByAgentId: privateTargetAgent.id,
+        updatedByAgentId: privateTargetAgent.id,
+      })
+      .returning()
+      .then((rows) => rows[0]!);
+    await db.insert(issueDocuments).values({
+      companyId: company.id,
+      issueId: issue.id,
+      documentId: doc.id,
+      key: "plan",
+    });
+    const asset = await db
+      .insert(assets)
+      .values({
+        companyId: company.id,
+        provider: "local_disk",
+        objectKey: `attachments/${randomUUID()}.txt`,
+        contentType: "text/plain",
+        byteSize: 12,
+        sha256: "abc123",
+        originalFilename: "note.txt",
+        createdByAgentId: privateTargetAgent.id,
+      })
+      .returning()
+      .then((rows) => rows[0]!);
+    await db.insert(issueAttachments).values({
+      companyId: company.id,
+      issueId: issue.id,
+      issueCommentId: comment.id,
+      assetId: asset.id,
+    });
+    await db.insert(issueWorkProducts).values({
+      companyId: company.id,
+      issueId: issue.id,
+      type: "url",
+      provider: "test",
+      title: "Preview",
+      url: "https://example.test/preview",
+      status: "ready",
+    });
+    await db.insert(activityLog).values({
+      companyId: company.id,
+      actorType: "agent",
+      actorId: privateTargetAgent.id,
+      agentId: privateTargetAgent.id,
+      action: "issue.updated",
+      entityType: "issue",
+      entityId: issue.id,
+      details: { source: "test" },
+    });
+
+    const app = await createApp(db, agentActor(company.id, readerAgent.id));
+
+    const [issueList, comments, docs, docDetail, attachments, activity, workProducts] = await Promise.all([
+      request(app).get(`/api/companies/${company.id}/issues`),
+      request(app).get(`/api/issues/${issue.id}/comments`),
+      request(app).get(`/api/issues/${issue.id}/documents`),
+      request(app).get(`/api/issues/${issue.id}/documents/plan`),
+      request(app).get(`/api/issues/${issue.id}/attachments`),
+      request(app).get(`/api/issues/${issue.id}/activity`),
+      request(app).get(`/api/issues/${issue.id}/work-products`),
+    ]);
+
+    expect(issueList.status, JSON.stringify(issueList.body)).toBe(200);
+    expect(issueList.body.items ?? issueList.body).toEqual(
+      expect.arrayContaining([expect.objectContaining({ id: issue.id })]),
+    );
+    expect(comments.status, JSON.stringify(comments.body)).toBe(200);
+    expect(comments.body).toEqual(expect.arrayContaining([expect.objectContaining({ id: comment.id })]));
+    expect(docs.status, JSON.stringify(docs.body)).toBe(200);
+    expect(docs.body).toEqual(expect.arrayContaining([expect.objectContaining({ key: "plan" })]));
+    expect(docDetail.status, JSON.stringify(docDetail.body)).toBe(200);
+    expect(docDetail.body.body ?? docDetail.body.latestBody).toContain("Shared plan body");
+    expect(attachments.status, JSON.stringify(attachments.body)).toBe(200);
+    expect(attachments.body).toEqual(expect.arrayContaining([expect.objectContaining({ id: expect.any(String) })]));
+    expect(activity.status, JSON.stringify(activity.body)).toBe(200);
+    expect(activity.body).toEqual(expect.arrayContaining([expect.objectContaining({ action: "issue.updated" })]));
+    expect(workProducts.status, JSON.stringify(workProducts.body)).toBe(200);
+    expect(workProducts.body).toEqual(expect.arrayContaining([expect.objectContaining({ title: "Preview" })]));
+  });
+
+  it("denies cross-company issue reads before private-agent grant evaluation can matter", async () => {
+    const sourceCompany = await seedCompany(db, "Source");
+    const targetCompany = await seedCompany(db, "Target");
+    const sourceAgent = await seedAgent(db, sourceCompany.id);
+    const privateTargetAgent = await seedAgent(db, targetCompany.id, {
+      permissions: {
+        authorizationPolicy: {
+          agentVisibility: { mode: "private", hiddenFromDefaultDirectory: true },
+          assignmentPolicy: { mode: "company_default" },
+          protectedAgent: { requiresApproval: false },
+        },
+      },
+    });
+    const issue = await db
+      .insert(issues)
+      .values({
+        companyId: targetCompany.id,
+        title: "Other company work",
+        status: "todo",
+        priority: "medium",
+        assigneeAgentId: privateTargetAgent.id,
+      })
+      .returning()
+      .then((rows) => rows[0]!);
+
+    const res = await request(await createApp(db, agentActor(sourceCompany.id, sourceAgent.id)))
+      .get(`/api/issues/${issue.id}`);
+
+    expect(res.status).toBe(403);
+    expect(res.body.error).toContain("Agent key cannot access another company");
+  });
+
+  it("allows same-company route assignment after upgrade but keeps private target assignment grant constrained", async () => {
+    const company = await seedCompany(db, "Assignment");
+    const actorAgent = await seedAgent(db, company.id);
+    const openTargetAgent = await seedAgent(db, company.id);
+    const privateTargetAgent = await seedAgent(db, company.id, {
+      permissions: {
+        authorizationPolicy: {
+          agentVisibility: { mode: "private", hiddenFromDefaultDirectory: true },
+          assignmentPolicy: { mode: "company_default" },
+          protectedAgent: { requiresApproval: false },
+          managedBy: "permissions-extension",
+        },
+      },
+    });
+    const app = await createApp(db, agentActor(company.id, actorAgent.id));
+
+    const openAssignment = await request(app)
+      .post(`/api/companies/${company.id}/issues`)
+      .send({ title: "Assignable after upgrade", assigneeAgentId: openTargetAgent.id });
+    expect(openAssignment.status, JSON.stringify(openAssignment.body)).toBe(201);
+
+    const deniedPrivateAssignment = await request(app)
+      .post(`/api/companies/${company.id}/issues`)
+      .send({ title: "Private target needs scope", assigneeAgentId: privateTargetAgent.id });
+    expect(deniedPrivateAssignment.status).toBe(403);
+    expect(deniedPrivateAssignment.body.error).toContain("private");
+
+    await db.insert(companyMemberships).values({
+      companyId: company.id,
+      principalType: "agent",
+      principalId: actorAgent.id,
+      status: "active",
+      membershipRole: "member",
+    });
+    await db.insert(principalPermissionGrants).values({
+      companyId: company.id,
+      principalType: "agent",
+      principalId: actorAgent.id,
+      permissionKey: "tasks:assign_scope",
+      scope: { assigneeAgentIds: [privateTargetAgent.id] },
+      grantedByUserId: null,
+    });
+
+    const allowedPrivateAssignment = await request(app)
+      .post(`/api/companies/${company.id}/issues`)
+      .send({ title: "Private target has explicit scope", assigneeAgentId: privateTargetAgent.id });
+    expect(allowedPrivateAssignment.status, JSON.stringify(allowedPrivateAssignment.body)).toBe(201);
+
+    const otherPrivateTargetAgent = await seedAgent(db, company.id, {
+      permissions: privateTargetAgent.permissions as Record<string, unknown>,
+    });
+    const deniedOutsideScope = await request(app)
+      .post(`/api/companies/${company.id}/issues`)
+      .send({ title: "Different private target stays denied", assigneeAgentId: otherPrivateTargetAgent.id });
+    expect(deniedOutsideScope.status).toBe(403);
+    expect(deniedOutsideScope.body.error).toContain("private");
+  });
+});