diff --git a/packages/cli/src/__tests__/project-context.test.ts b/packages/cli/src/__tests__/project-context.test.ts
index ea87496ab..bad85ef47 100644
--- a/packages/cli/src/__tests__/project-context.test.ts
+++ b/packages/cli/src/__tests__/project-context.test.ts
@@ -22,6 +22,7 @@ describe("project-context", () => {
   let homeDir: string;
   let central: CentralCore;
   const originalHome = process.env.HOME;
+  const createdProjectIds: string[] = [];
 
   beforeEach(async () => {
     tempDir = mkdtempSync(join(tmpdir(), "kb-test-"));
@@ -32,8 +33,26 @@ describe("project-context", () => {
   });
 
   afterEach(async () => {
-    await central.close();
+    // Teardown order: entity cleanup first, then infrastructure, then filesystem
+    // Unregister all tracked projects first
+    for (const projectId of createdProjectIds) {
+      try {
+        await central.unregisterProject(projectId);
+      } catch {
+        // Ignore cleanup errors for already-removed entities
+      }
+    }
+    createdProjectIds.length = 0;
+
+    // Close CentralCore before filesystem cleanup
+    try {
+      await central.close();
+    } catch {
+      // Ignore close errors
+    }
     clearStoreCache();
+
+    // Filesystem cleanup last
     try {
       rmSync(tempDir, { recursive: true, force: true });
       rmSync(homeDir, { recursive: true, force: true });
@@ -61,6 +80,7 @@ describe("project-context", () => {
         name: "my-project",
         path: resolve(projectPath),
       });
+      createdProjectIds.push(project.id);
 
       const found = await detectProjectFromCwd(projectPath, central);
 
@@ -78,6 +98,7 @@ describe("project-context", () => {
         name: "my-project",
         path: resolve(projectPath),
       });
+      createdProjectIds.push(project.id);
 
       const found = await detectProjectFromCwd(subDir, central);
 
diff --git a/packages/core/src/__tests__/agent-instructions-bundle.test.ts b/packages/core/src/__tests__/agent-instructions-bundle.test.ts
index 6ab6fad77..bc9629cab 100644
--- a/packages/core/src/__tests__/agent-instructions-bundle.test.ts
+++ b/packages/core/src/__tests__/agent-instructions-bundle.test.ts
@@ -7,6 +7,7 @@ import { AgentStore } from "../agent-store.js";
 describe("AgentStore — instructions bundle", () => {
   let testDir: string;
   let store: AgentStore;
+  const createdAgentIds: string[] = [];
 
   beforeEach(async () => {
     testDir = await mkdtemp(join(tmpdir(), "agent-instructions-bundle-test-"));
@@ -15,7 +16,23 @@ describe("AgentStore — instructions bundle", () => {
   });
 
   afterEach(async () => {
-    await rm(testDir, { recursive: true, force: true });
+    // Teardown order: entity cleanup first, then filesystem
+    // Delete all created agents explicitly
+    for (const agentId of createdAgentIds) {
+      try {
+        await store.deleteAgent(agentId);
+      } catch {
+        // Ignore cleanup errors for already-removed entities
+      }
+    }
+    createdAgentIds.length = 0;
+
+    // Filesystem cleanup last
+    try {
+      await rm(testDir, { recursive: true, force: true });
+    } catch {
+      // Ignore cleanup errors
+    }
   });
 
   it("persists bundleConfig through create + load roundtrip", async () => {
@@ -28,6 +45,7 @@ describe("AgentStore — instructions bundle", () => {
         files: ["AGENTS.md", "STYLE.md"],
       },
     });
+    createdAgentIds.push(created.id);
 
     expect(created.bundleConfig).toEqual({
       mode: "managed",
@@ -41,11 +59,13 @@ describe("AgentStore — instructions bundle", () => {
 
   it("getInstructionsDir returns the managed bundle directory path", async () => {
     const agent = await store.createAgent({ name: "dir-agent", role: "executor" });
+    createdAgentIds.push(agent.id);
     expect(store.getInstructionsDir(agent.id)).toBe(join(testDir, "agents", `${agent.id}-instructions`));
   });
 
   it("listBundleFiles returns empty for missing directory and sorted .md files only", async () => {
     const agent = await store.createAgent({ name: "list-agent", role: "executor" });
+    createdAgentIds.push(agent.id);
 
     expect(await store.listBundleFiles(agent.id)).toEqual([]);
 
@@ -61,6 +81,7 @@ describe("AgentStore — instructions bundle", () => {
 
   it("readBundleFile reads content and rejects missing/traversal paths", async () => {
     const agent = await store.createAgent({ name: "read-agent", role: "executor" });
+    createdAgentIds.push(agent.id);
 
     await store.writeBundleFile(agent.id, "AGENTS.md", "Hello bundle");
     await expect(store.readBundleFile(agent.id, "AGENTS.md")).resolves.toBe("Hello bundle");
@@ -71,6 +92,7 @@ describe("AgentStore — instructions bundle", () => {
 
   it("writeBundleFile creates directories, overwrites, validates paths, and enforces max file count", async () => {
     const agent = await store.createAgent({ name: "write-agent", role: "executor" });
+    createdAgentIds.push(agent.id);
     const dir = store.getInstructionsDir(agent.id);
 
     await store.writeBundleFile(agent.id, "AGENTS.md", "first");
@@ -93,6 +115,7 @@ describe("AgentStore — instructions bundle", () => {
 
   it("deleteBundleFile removes files and throws when missing", async () => {
     const agent = await store.createAgent({ name: "delete-agent", role: "executor" });
+    createdAgentIds.push(agent.id);
     const filePath = join(store.getInstructionsDir(agent.id), "AGENTS.md");
 
     await store.writeBundleFile(agent.id, "AGENTS.md", "to-delete");
@@ -104,6 +127,7 @@ describe("AgentStore — instructions bundle", () => {
 
   it("setBundleConfig validates input and creates managed directory", async () => {
     const agent = await store.createAgent({ name: "config-agent", role: "executor" });
+    createdAgentIds.push(agent.id);
 
     const managed = await store.setBundleConfig(agent.id, {
       mode: "managed",
@@ -143,6 +167,7 @@ describe("AgentStore — instructions bundle", () => {
       role: "executor",
       instructionsText: "Legacy text content",
     });
+    createdAgentIds.push(agent.id);
 
     const migrated = await store.migrateLegacyInstructions(agent.id);
 
@@ -166,6 +191,7 @@ describe("AgentStore — instructions bundle", () => {
       role: "executor",
       instructionsPath: sourcePath,
     });
+    createdAgentIds.push(agent.id);
 
     const migrated = await store.migrateLegacyInstructions(agent.id);
 
@@ -189,6 +215,7 @@ describe("AgentStore — instructions bundle", () => {
       instructionsText: "Primary inline content",
       instructionsPath: sourcePath,
     });
+    createdAgentIds.push(agent.id);
 
     const migrated = await store.migrateLegacyInstructions(agent.id);
 
@@ -215,6 +242,7 @@ describe("AgentStore — instructions bundle", () => {
       },
       instructionsText: "should-stay",
     });
+    createdAgentIds.push(agent.id);
 
     const migrated = await store.migrateLegacyInstructions(agent.id);
 
@@ -231,6 +259,7 @@ describe("AgentStore — instructions bundle", () => {
       name: "no-legacy",
       role: "executor",
     });
+    createdAgentIds.push(agent.id);
 
     const migrated = await store.migrateLegacyInstructions(agent.id);
 
diff --git a/packages/core/src/__tests__/agent-instructions.test.ts b/packages/core/src/__tests__/agent-instructions.test.ts
index 5240f9e8e..39e29c948 100644
--- a/packages/core/src/__tests__/agent-instructions.test.ts
+++ b/packages/core/src/__tests__/agent-instructions.test.ts
@@ -7,6 +7,7 @@ import { AgentStore } from "../agent-store.js";
 describe("AgentStore — instructions fields", () => {
   let testDir: string;
   let store: AgentStore;
+  const createdAgentIds: string[] = [];
 
   beforeEach(async () => {
     testDir = await mkdtemp(join(tmpdir(), "agent-instructions-test-"));
@@ -15,7 +16,23 @@ describe("AgentStore — instructions fields", () => {
   });
 
   afterEach(async () => {
-    await rm(testDir, { recursive: true, force: true });
+    // Teardown order: entity cleanup first, then filesystem
+    // Delete all created agents explicitly
+    for (const agentId of createdAgentIds) {
+      try {
+        await store.deleteAgent(agentId);
+      } catch {
+        // Ignore cleanup errors for already-removed entities
+      }
+    }
+    createdAgentIds.length = 0;
+
+    // Filesystem cleanup last
+    try {
+      await rm(testDir, { recursive: true, force: true });
+    } catch {
+      // Ignore cleanup errors
+    }
   });
 
   it("creates an agent with instructionsText", async () => {
@@ -24,6 +41,7 @@ describe("AgentStore — instructions fields", () => {
       role: "executor",
       instructionsText: "Always use TypeScript strict mode.",
     });
+    createdAgentIds.push(agent.id);
 
     expect(agent.instructionsText).toBe("Always use TypeScript strict mode.");
     expect(agent.instructionsPath).toBeUndefined();
@@ -35,6 +53,7 @@ describe("AgentStore — instructions fields", () => {
       role: "executor",
       instructionsPath: ".fusion/agents/custom.md",
     });
+    createdAgentIds.push(agent.id);
 
     expect(agent.instructionsPath).toBe(".fusion/agents/custom.md");
     expect(agent.instructionsText).toBeUndefined();
@@ -47,6 +66,7 @@ describe("AgentStore — instructions fields", () => {
       instructionsText: "Check for security issues.",
       instructionsPath: ".fusion/agents/reviewer.md",
     });
+    createdAgentIds.push(agent.id);
 
     expect(agent.instructionsText).toBe("Check for security issues.");
     expect(agent.instructionsPath).toBe(".fusion/agents/reviewer.md");
@@ -57,6 +77,7 @@ describe("AgentStore — instructions fields", () => {
       name: "test-agent",
       role: "executor",
     });
+    createdAgentIds.push(agent.id);
 
     expect(agent.instructionsText).toBeUndefined();
     expect(agent.instructionsPath).toBeUndefined();
@@ -68,6 +89,7 @@ describe("AgentStore — instructions fields", () => {
       role: "executor",
       instructionsText: "Always write tests.",
     });
+    createdAgentIds.push(created.id);
 
     const loaded = await store.getAgent(created.id);
     expect(loaded).not.toBeNull();
@@ -80,6 +102,7 @@ describe("AgentStore — instructions fields", () => {
       role: "executor",
       instructionsPath: ".fusion/agents/instructions.md",
     });
+    createdAgentIds.push(created.id);
 
     const loaded = await store.getAgent(created.id);
     expect(loaded).not.toBeNull();
@@ -91,6 +114,7 @@ describe("AgentStore — instructions fields", () => {
       name: "test-agent",
       role: "executor",
     });
+    createdAgentIds.push(agent.id);
 
     const updated = await store.updateAgent(agent.id, {
       instructionsText: "Use functional programming patterns.",
@@ -104,6 +128,7 @@ describe("AgentStore — instructions fields", () => {
       name: "test-agent",
       role: "executor",
     });
+    createdAgentIds.push(agent.id);
 
     const updated = await store.updateAgent(agent.id, {
       instructionsPath: ".fusion/agents/new-instructions.md",
@@ -118,6 +143,7 @@ describe("AgentStore — instructions fields", () => {
       role: "executor",
       instructionsText: "Some instructions",
     });
+    createdAgentIds.push(agent.id);
 
     const updated = await store.updateAgent(agent.id, {
       instructionsText: "",
@@ -133,6 +159,7 @@ describe("AgentStore — instructions fields", () => {
       role: "executor",
       instructionsPath: ".fusion/agents/old.md",
     });
+    createdAgentIds.push(agent.id);
 
     const updated = await store.updateAgent(agent.id, {
       instructionsPath: "",
@@ -148,6 +175,7 @@ describe("AgentStore — instructions fields", () => {
       instructionsText: "Old text",
       instructionsPath: "old.md",
     });
+    createdAgentIds.push(agent.id);
 
     const updated = await store.updateAgent(agent.id, {
       instructionsText: "New text",
@@ -170,6 +198,7 @@ describe("AgentStore — instructions fields", () => {
       title: "My Executor",
       instructionsText: "Initial",
     });
+    createdAgentIds.push(agent.id);
 
     const updated = await store.updateAgent(agent.id, {
       instructionsText: "Updated",
@@ -188,6 +217,7 @@ describe("AgentStore — instructions fields", () => {
       instructionsText: "Cached instructions",
       instructionsPath: ".fusion/cached.md",
     });
+    createdAgentIds.push(agent.id);
 
     const cached = store.getCachedAgent(agent.id);
     expect(cached).not.toBeNull();
diff --git a/packages/core/src/__tests__/central-integration.test.ts b/packages/core/src/__tests__/central-integration.test.ts
index 63f878f63..5ae1d3d5b 100644
--- a/packages/core/src/__tests__/central-integration.test.ts
+++ b/packages/core/src/__tests__/central-integration.test.ts
@@ -30,9 +30,30 @@ describe("CentralCore Integration", () => {
   });
 
   afterAll(async () => {
-    // Cleanup
-    await central.close();
-    rmSync(tempDir, { recursive: true, force: true });
+    // Teardown order: entity cleanup first, then infrastructure, then filesystem
+    // Unregister all tracked projects first (not just a subset from assertions)
+    for (const project of projects) {
+      try {
+        await central.unregisterProject(project.id);
+      } catch {
+        // Ignore cleanup errors for already-removed entities
+      }
+    }
+    projects.length = 0;
+
+    // Close CentralCore before filesystem cleanup
+    try {
+      await central.close();
+    } catch {
+      // Ignore close errors
+    }
+
+    // Filesystem cleanup last
+    try {
+      rmSync(tempDir, { recursive: true, force: true });
+    } catch {
+      // Ignore cleanup errors
+    }
   });
 
   it("should register multiple projects", async () => {