diff --git a/src/mcp/server.ts b/src/mcp/server.ts
index 559512e02..927fd52b7 100644
--- a/src/mcp/server.ts
+++ b/src/mcp/server.ts
@@ -21,6 +21,23 @@ import { gcSessionContextState } from '../core/context/session-state.ts';
 import { makeContextPackIpcHandler } from './context-pack-handler.ts';
 import { logTurnContextDeliveryFireAndForget } from '../core/context/volunteer-events.ts';
 
+export async function resolveMcpStdioSourceScope(
+  engine: BrainEngine,
+  cwd: string = process.cwd(),
+): Promise<{ sourceId: string; localFederatedSourceIds?: string[] }> {
+  try {
+    const { resolveSourceWithTier, localFederatedSourceIds } = await import('../core/source-resolver.ts');
+    const resolved = await resolveSourceWithTier(engine, null, cwd);
+    const federated = await localFederatedSourceIds(engine, resolved.source_id, resolved.tier);
+    return {
+      sourceId: resolved.source_id,
+      ...(federated ? { localFederatedSourceIds: federated } : {}),
+    };
+  } catch {
+    return { sourceId: process.env.GBRAIN_SOURCE || 'default' };
+  }
+}
+
 export async function startMcpServer(engine: BrainEngine, opts: { surface?: McpSurface } = {}) {
   const server = new Server(
     { name: 'gbrain', version: VERSION },
@@ -48,20 +65,11 @@ export async function startMcpServer(engine: BrainEngine, opts: { surface?: McpS
   // shape and cast through `any` (the SDK accepts it via the ServerResult union).
   server.setRequestHandler(CallToolRequestSchema, async (request: any): Promise<any> => {
     const { name, arguments: params } = request.params;
-    // #3242: when the operator didn't pin a source via GBRAIN_SOURCE, stdio
-    // reads span every `config.federated = true` source (same visibility set
-    // as unqualified local CLI reads). GBRAIN_SOURCE set = explicit scope,
-    // no widening. Best-effort: a resolver failure keeps the scalar scope.
-    // ponytail: one tiny SELECT per tool call; cache it if it ever shows up.
-    let localFederated: string[] | undefined;
-    try {
-      const { localFederatedSourceIds } = await import('../core/source-resolver.ts');
-      localFederated = await localFederatedSourceIds(
-        engine,
-        process.env.GBRAIN_SOURCE || 'default',
-        process.env.GBRAIN_SOURCE ? 'env' : 'seed_default',
-      );
-    } catch { /* scalar scope stands */ }
+    // #3242 / #3906: stdio resolves its source through the same ambient chain
+    // as local CLI dispatch: GBRAIN_SOURCE, then .gbrain-source, then the
+    // non-explicit fallback tiers. Non-explicit tiers may widen to federated
+    // local reads; explicit/env/dotfile scopes stay scalar.
+    const sourceScope = await resolveMcpStdioSourceScope(engine);
     // v0.28: stdio MCP has no per-token auth (local pipe). Default the
     // takes-holder allow-list to ['world'] so agent-facing callers don't
     // see private hunches via takes_list / takes_search / query. Operators
@@ -83,11 +91,10 @@ export async function startMcpServer(engine: BrainEngine, opts: { surface?: McpS
       transport: 'stdio',
       takesHoldersAllowList: ['world'],
       ...(sessionId ? { sessionId } : {}),
-      // v0.31: source defaults to 'default' for stdio (no per-token scope).
-      // Operators who want a different source on stdio MCP should set
-      // GBRAIN_SOURCE in the env or use --source via `gbrain call`.
-      sourceId: process.env.GBRAIN_SOURCE || 'default',
-      ...(localFederated ? { localFederatedSourceIds: localFederated } : {}),
+      sourceId: sourceScope.sourceId,
+      ...(sourceScope.localFederatedSourceIds
+        ? { localFederatedSourceIds: sourceScope.localFederatedSourceIds }
+        : {}),
       // v0.31 (eD3): _meta.brain_hot_memory injection so Claude Desktop /
       // Code see the brain's relevant hot memory automatically alongside
       // every tool-call response. Best-effort; absorbs errors.
@@ -112,7 +119,7 @@ export async function startMcpServer(engine: BrainEngine, opts: { surface?: McpS
     const cfg = loadConfig();
     if (cfg?.engine === 'pglite' && cfg.database_path) {
       resolveSocket = resolveSocketPath(cfg.database_path);
-      const defaultSource = process.env.GBRAIN_SOURCE || 'default';
+      const { sourceId: defaultSource } = await resolveMcpStdioSourceScope(engine);
       // [S3#6] turn_context requires the shared secret from the data dir
       // (created 0600 here if absent). If the secret can't be provisioned,
       // turn_context stays fail-closed ('unauthorized') while the secret-free
@@ -194,8 +201,9 @@ export async function startMcpServer(engine: BrainEngine, opts: { surface?: McpS
   let startupSweep: { cancel: () => void } | null = null;
   try {
     const { armStartupSweep } = await import('../core/sweep.ts');
+    const { sourceId } = await resolveMcpStdioSourceScope(engine);
     startupSweep = armStartupSweep(engine, {
-      sourceId: process.env.GBRAIN_SOURCE || 'default',
+      sourceId,
     });
   } catch {
     /* startup sweep is best-effort; never block serve */
diff --git a/test/mcp-stdio-source-resolution.test.ts b/test/mcp-stdio-source-resolution.test.ts
new file mode 100644
index 000000000..50a8c348d
--- /dev/null
+++ b/test/mcp-stdio-source-resolution.test.ts
@@ -0,0 +1,73 @@
+import { describe, test, expect, afterEach } from 'bun:test';
+import { chmodSync, mkdtempSync, rmSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import type { BrainEngine } from '../src/core/engine.ts';
+import { resolveMcpStdioSourceScope } from '../src/mcp/server.ts';
+import { withEnv } from './helpers/with-env.ts';
+
+function makeEngine(registeredSources: string[]): BrainEngine {
+  return {
+    kind: 'pglite',
+    executeRaw: async <T>(sql: string, params?: unknown[]): Promise<T[]> => {
+      if (sql.includes('SELECT id FROM sources WHERE id = $1')) {
+        const id = params?.[0];
+        return (typeof id === 'string' && registeredSources.includes(id)
+          ? [{ id } as T]
+          : []);
+      }
+      if (sql.includes('SELECT id, local_path FROM sources')) return [];
+      if (sql.includes('SELECT id, config, archived FROM sources')) {
+        return registeredSources.map(id => ({ id, config: null, archived: false }) as T);
+      }
+      return [];
+    },
+    getConfig: async () => null,
+  } as unknown as BrainEngine;
+}
+
+function writeSourceDotfile(dir: string, sourceId: string): void {
+  const path = join(dir, '.gbrain-source');
+  writeFileSync(path, `${sourceId}\n`);
+  chmodSync(path, 0o600);
+}
+
+describe('stdio MCP source resolution', () => {
+  const scratchDirs: string[] = [];
+
+  afterEach(() => {
+    for (const dir of scratchDirs.splice(0)) {
+      rmSync(dir, { recursive: true, force: true });
+    }
+  });
+
+  test('honors .gbrain-source when GBRAIN_SOURCE is absent', async () => {
+    const dir = mkdtempSync(join(tmpdir(), 'gbrain-mcp-source-'));
+    scratchDirs.push(dir);
+    writeSourceDotfile(dir, 'team-alpha');
+
+    await withEnv({ GBRAIN_SOURCE: undefined }, async () => {
+      const scope = await resolveMcpStdioSourceScope(
+        makeEngine(['default', 'team-alpha']),
+        dir,
+      );
+
+      expect(scope).toEqual({ sourceId: 'team-alpha' });
+    });
+  });
+
+  test('GBRAIN_SOURCE wins over .gbrain-source', async () => {
+    const dir = mkdtempSync(join(tmpdir(), 'gbrain-mcp-source-'));
+    scratchDirs.push(dir);
+    writeSourceDotfile(dir, 'team-alpha');
+
+    await withEnv({ GBRAIN_SOURCE: 'env-source' }, async () => {
+      const scope = await resolveMcpStdioSourceScope(
+        makeEngine(['default', 'team-alpha', 'env-source']),
+        dir,
+      );
+
+      expect(scope).toEqual({ sourceId: 'env-source' });
+    });
+  });
+});