diff --git a/v3/@claude-flow/cli/__tests__/terminal-encryption.test.ts b/v3/@claude-flow/cli/__tests__/terminal-encryption.test.ts
new file mode 100644
index 0000000000..692c7f5f8f
--- /dev/null
+++ b/v3/@claude-flow/cli/__tests__/terminal-encryption.test.ts
@@ -0,0 +1,172 @@
+/**
+ * Integration test for ADR-096 Phase 3: terminal-tools wired to vault.
+ *
+ * Mirrors session-encryption.test.ts structure: full save → on-disk →
+ * load round-trip across plaintext + encrypted modes plus the migration
+ * path (legacy plaintext readable after the gate flips on).
+ *
+ * Terminal stores are higher-stakes than session JSON because the command
+ * history routinely contains pasted shell commands with credentials —
+ * the on-disk-doesn't-leak-the-secret assertion is therefore stricter
+ * than the equivalent session test (we plant a known credential string
+ * and assert it never appears in the encrypted bytes).
+ */
+
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+import { mkdtempSync, readFileSync, rmSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { randomBytes } from 'node:crypto';
+
+import { terminalTools } from '../src/mcp-tools/terminal-tools.js';
+import { MAGIC, isEncryptedBlob } from '../src/encryption/vault.js';
+
+const SAVED_ENV: Record<string, string | undefined> = {};
+function saveEnv(...names: string[]) {
+  for (const n of names) SAVED_ENV[n] = process.env[n];
+}
+function restoreEnv() {
+  for (const [n, v] of Object.entries(SAVED_ENV)) {
+    if (v === undefined) delete process.env[n];
+    else process.env[n] = v;
+  }
+}
+
+const terminalCreateTool = terminalTools.find(t => t.name === 'terminal_create')!;
+const terminalListTool = terminalTools.find(t => t.name === 'terminal_list')!;
+
+function getStoreFile(workdir: string): string {
+  return join(workdir, '.claude-flow', 'terminals', 'store.json');
+}
+
+async function runCreate(name: string) {
+  return terminalCreateTool.handler({ name } as Record<string, unknown>);
+}
+
+describe('terminal-tools encryption-at-rest (ADR-096 Phase 3)', () => {
+  let workdir: string;
+  let cwdSpy: ReturnType<typeof vi.spyOn> | null = null;
+
+  beforeEach(() => {
+    saveEnv('CLAUDE_FLOW_ENCRYPT_AT_REST', 'CLAUDE_FLOW_ENCRYPTION_KEY');
+    workdir = mkdtempSync(join(tmpdir(), 'term-enc-'));
+    cwdSpy = vi.spyOn(process, 'cwd').mockReturnValue(workdir);
+  });
+
+  afterEach(() => {
+    cwdSpy?.mockRestore();
+    rmSync(workdir, { recursive: true, force: true });
+    restoreEnv();
+  });
+
+  describe('encryption disabled (legacy plaintext)', () => {
+    beforeEach(() => {
+      delete process.env.CLAUDE_FLOW_ENCRYPT_AT_REST;
+      delete process.env.CLAUDE_FLOW_ENCRYPTION_KEY;
+    });
+
+    it('writes plaintext JSON to disk', async () => {
+      await runCreate('legacy-term');
+      const onDisk = readFileSync(getStoreFile(workdir));
+      // First byte is "{" not "R" — plaintext JSON
+      expect(onDisk[0]).toBe(0x7b);
+      expect(isEncryptedBlob(onDisk)).toBe(false);
+      const parsed = JSON.parse(onDisk.toString('utf-8')) as {
+        sessions: Record<string, { name: string }>;
+      };
+      const names = Object.values(parsed.sessions).map(s => s.name);
+      expect(names).toContain('legacy-term');
+    });
+
+    it('round-trips create → list', async () => {
+      await runCreate('rt-plain');
+      const result = (await terminalListTool.handler({} as Record<string, unknown>)) as {
+        sessions?: Array<{ name?: string }>;
+      };
+      const names = (result.sessions ?? []).map(s => s?.name).filter(Boolean);
+      expect(names).toContain('rt-plain');
+    });
+  });
+
+  describe('encryption enabled (RFE1 wire format)', () => {
+    beforeEach(() => {
+      process.env.CLAUDE_FLOW_ENCRYPT_AT_REST = '1';
+      process.env.CLAUDE_FLOW_ENCRYPTION_KEY = randomBytes(32).toString('hex');
+    });
+
+    it('writes a blob that starts with the RFE1 magic', async () => {
+      await runCreate('encrypted-term');
+      const onDisk = readFileSync(getStoreFile(workdir));
+      expect(onDisk.subarray(0, 4)).toEqual(MAGIC);
+      expect(isEncryptedBlob(onDisk)).toBe(true);
+    });
+
+    it('does not leak the plaintext name into the on-disk bytes', async () => {
+      // Defense-in-depth: terminal stores carry pasted credentials in the
+      // history field. If encryption ran, NO part of the plaintext should
+      // appear in the on-disk file.
+      const secretName = `creds-${randomBytes(8).toString('hex')}`;
+      await runCreate(secretName);
+      const onDisk = readFileSync(getStoreFile(workdir));
+      expect(onDisk.includes(Buffer.from(secretName, 'utf-8'))).toBe(false);
+    });
+
+    it('round-trips create → list using the same key', async () => {
+      await runCreate('rt-enc');
+      const result = (await terminalListTool.handler({} as Record<string, unknown>)) as {
+        sessions?: Array<{ name?: string }>;
+      };
+      const names = (result.sessions ?? []).map(s => s?.name).filter(Boolean);
+      expect(names).toContain('rt-enc');
+    });
+  });
+
+  describe('migration: legacy plaintext readable after gate flips on', () => {
+    it('reads a legacy plaintext store after encryption is enabled', async () => {
+      // Step 1: write plaintext (gate off)
+      delete process.env.CLAUDE_FLOW_ENCRYPT_AT_REST;
+      delete process.env.CLAUDE_FLOW_ENCRYPTION_KEY;
+      await runCreate('legacy-readable');
+
+      // Step 2: flip encryption on for the read
+      process.env.CLAUDE_FLOW_ENCRYPT_AT_REST = '1';
+      process.env.CLAUDE_FLOW_ENCRYPTION_KEY = randomBytes(32).toString('hex');
+
+      // Step 3: list should still find the legacy session via the
+      // magic-byte sniff (legacy file → not encrypted → returned as-is)
+      const result = (await terminalListTool.handler({} as Record<string, unknown>)) as {
+        sessions?: Array<{ name?: string }>;
+      };
+      const names = (result.sessions ?? []).map(s => s?.name).filter(Boolean);
+      expect(names).toContain('legacy-readable');
+    });
+  });
+
+  describe('mixed: same store, plaintext write then encrypted overwrite', () => {
+    it('rewrites the file as encrypted on the next write after gate flips on', async () => {
+      // Step 1: legacy plaintext write
+      delete process.env.CLAUDE_FLOW_ENCRYPT_AT_REST;
+      delete process.env.CLAUDE_FLOW_ENCRYPTION_KEY;
+      await runCreate('plain-first');
+      expect(isEncryptedBlob(readFileSync(getStoreFile(workdir)))).toBe(false);
+
+      // Step 2: enable encryption and add a second session — saveTerminalStore
+      // rewrites the WHOLE file, so the result is encrypted bytes that
+      // contain both sessions.
+      process.env.CLAUDE_FLOW_ENCRYPT_AT_REST = '1';
+      process.env.CLAUDE_FLOW_ENCRYPTION_KEY = randomBytes(32).toString('hex');
+      await runCreate('encrypted-second');
+
+      const onDisk = readFileSync(getStoreFile(workdir));
+      expect(isEncryptedBlob(onDisk)).toBe(true);
+
+      // Both sessions still visible via list (decrypts on read)
+      const result = (await terminalListTool.handler({} as Record<string, unknown>)) as {
+        sessions?: Array<{ name?: string }>;
+      };
+      const names = (result.sessions ?? []).map(s => s?.name).filter(Boolean);
+      expect(names).toContain('plain-first');
+      expect(names).toContain('encrypted-second');
+    });
+  });
+});
diff --git a/v3/@claude-flow/cli/src/mcp-tools/terminal-tools.ts b/v3/@claude-flow/cli/src/mcp-tools/terminal-tools.ts
index af5c90608c..782f4a25d9 100644
--- a/v3/@claude-flow/cli/src/mcp-tools/terminal-tools.ts
+++ b/v3/@claude-flow/cli/src/mcp-tools/terminal-tools.ts
@@ -5,8 +5,12 @@
  */
 
 import { type MCPTool, getProjectCwd } from './types.js';
-import { existsSync, readFileSync } from 'node:fs';
-import { mkdirRestricted, writeFileRestricted } from '../fs-secure.js';
+import { existsSync } from 'node:fs';
+import {
+  mkdirRestricted,
+  readFileMaybeEncrypted,
+  writeFileRestricted,
+} from '../fs-secure.js';
 import { validateEnv, validateIdentifier, validatePath, validateText } from './validate-input.js';
 import { join } from 'node:path';
 import { execSync } from 'node:child_process';
@@ -51,7 +55,10 @@ function loadTerminalStore(): TerminalStore {
   try {
     const path = getTerminalPath();
     if (existsSync(path)) {
-      return JSON.parse(readFileSync(path, 'utf-8'));
+      // ADR-096 Phase 3: readFileMaybeEncrypted handles both legacy
+      // plaintext stores and post-migration encrypted ones via the RFE1
+      // magic-byte sniff.
+      return JSON.parse(readFileMaybeEncrypted(path, 'utf-8'));
     }
   } catch {
     // Return empty store
@@ -62,8 +69,15 @@ function loadTerminalStore(): TerminalStore {
 function saveTerminalStore(store: TerminalStore): void {
   ensureTerminalDir();
   // audit_1776853149979: terminal command history can contain credentials
-  // pasted into commands; restrict to owner read/write.
-  writeFileRestricted(getTerminalPath(), JSON.stringify(store, null, 2));
+  // pasted into commands; restrict to owner read/write (mode 0600).
+  // ADR-096 Phase 3: opt-in AES-256-GCM encrypt-at-rest. Honored only
+  // when CLAUDE_FLOW_ENCRYPT_AT_REST is set; otherwise legacy plaintext
+  // path runs unchanged.
+  writeFileRestricted(
+    getTerminalPath(),
+    JSON.stringify(store, null, 2),
+    { encrypt: true },
+  );
 }
 
 export const terminalTools: MCPTool[] = [