diff --git a/packages/mongodb-runner/src/mongocluster.spec.ts b/packages/mongodb-runner/src/mongocluster.spec.ts
index 841eed06..156b3ea7 100644
--- a/packages/mongodb-runner/src/mongocluster.spec.ts
+++ b/packages/mongodb-runner/src/mongocluster.spec.ts
@@ -258,10 +258,10 @@ describe('MongoCluster', function () {
       secondaries: 0,
     });
     cluster = await MongoCluster.deserialize(cluster.serialize());
-    const { ok } = await cluster.withClient(async (client) => {
-      return await client.db('admin').command({ ping: 1 });
+    const doc = await cluster.withClient(async (client) => {
+      return await client.db('config').collection('mongodbrunner').findOne();
     });
-    expect(ok).to.equal(1);
+    expect(doc?._id).to.be.a('string');
     await cluster.close();
   });
 });
diff --git a/packages/mongodb-runner/src/mongoserver.ts b/packages/mongodb-runner/src/mongoserver.ts
index 505d6184..234a8513 100644
--- a/packages/mongodb-runner/src/mongoserver.ts
+++ b/packages/mongodb-runner/src/mongoserver.ts
@@ -9,11 +9,11 @@ import {
   isFailureToSetupListener,
 } from './mongologreader';
 import { Readable } from 'stream';
-import type { Document } from 'mongodb';
+import type { Document, MongoClientOptions } from 'mongodb';
 import { MongoClient } from 'mongodb';
 import path from 'path';
 import { once } from 'events';
-import { uuid, debug } from './util';
+import { uuid, debug, pick } from './util';
 
 export interface MongoServerOptions {
   binDir?: string;
@@ -24,32 +24,52 @@ export interface MongoServerOptions {
   docker?: string | string[]; // Image or docker options
 }
 
+interface SerializedServerProperties {
+  _id: string;
+  pid?: number;
+  port?: number;
+  dbPath?: string;
+  startTime: string;
+  hasInsertedMetadataCollEntry: boolean;
+}
+
 export class MongoServer {
+  private uuid: string = uuid();
   private buildInfo?: Document;
   private childProcess?: ChildProcess;
   private pid?: number;
   private port?: number;
   private dbPath?: string;
   private closing = false;
+  private startTime = new Date().toISOString();
+  private hasInsertedMetadataCollEntry = false;
 
   private constructor() {
     /* see .start() */
   }
 
-  serialize(): unknown /* JSON-serializable */ {
+  serialize(): SerializedServerProperties {
     return {
+      _id: this.uuid,
       pid: this.pid,
       port: this.port,
       dbPath: this.dbPath,
+      startTime: this.startTime,
+      hasInsertedMetadataCollEntry: this.hasInsertedMetadataCollEntry,
     };
   }
 
-  static async deserialize(serialized: any): Promise<MongoServer> {
+  static async deserialize(
+    serialized: SerializedServerProperties,
+  ): Promise<MongoServer> {
     const srv = new MongoServer();
-    srv.pid = serialized.pid;
+    srv.uuid = serialized._id;
     srv.port = serialized.port;
-    srv.dbPath = serialized.dbPath;
-    await srv._populateBuildInfo();
+    srv.closing = !!(await srv._populateBuildInfo('restore-check'));
+    if (!srv.closing) {
+      srv.pid = serialized.pid;
+      srv.dbPath = serialized.dbPath;
+    }
     return srv;
   }
 
@@ -116,7 +136,7 @@ export class MongoServer {
     const srv = new MongoServer();
 
     if (!options.docker) {
-      const dbPath = path.join(options.tmpDir, `db-${uuid()}`);
+      const dbPath = path.join(options.tmpDir, `db-${srv.uuid}`);
       await fs.mkdir(dbPath, { recursive: true });
       srv.dbPath = dbPath;
     }
@@ -234,7 +254,10 @@ export class MongoServer {
       logEntryStream.resume();
 
       srv.port = port;
-      await srv._populateBuildInfo();
+      const buildInfoError = await srv._populateBuildInfo('insert-new');
+      if (buildInfoError) {
+        debug('failed to get buildInfo', buildInfoError);
+      }
     } catch (err) {
       await srv.close();
       throw err;
@@ -270,24 +293,83 @@ export class MongoServer {
     this.dbPath = undefined;
   }
 
-  private async _populateBuildInfo(): Promise<void> {
-    if (this.buildInfo?.version) return;
-    this.buildInfo = await this.withClient(
-      async (client) => await client.db('admin').command({ buildInfo: 1 }),
-    );
+  private async _ensureMatchingMetadataColl(
+    client: MongoClient,
+    mode: 'insert-new' | 'restore-check',
+  ): Promise<void> {
+    const hello = await client.db('admin').command({ hello: 1 });
+    const isMongoS = hello.msg === 'isdbgrid';
+    const insertedInfo = pick(this.serialize(), [
+      '_id',
+      'pid',
+      'port',
+      'dbPath',
+      'startTime',
+    ]);
+    const runnerColl = client
+      .db(isMongoS ? 'config' : 'local')
+      .collection<
+        Omit<SerializedServerProperties, 'hasInsertedMetadataCollEntry'>
+      >('mongodbrunner');
+    debug('ensuring metadata collection entry', insertedInfo, { isMongoS });
+    if (mode === 'insert-new') {
+      await runnerColl.insertOne(insertedInfo);
+      debug('inserted metadata collection entry', insertedInfo);
+      this.hasInsertedMetadataCollEntry = true;
+    } else {
+      if (!this.hasInsertedMetadataCollEntry) {
+        debug(
+          'skipping metadata collection match check as we never inserted metadata',
+        );
+        return;
+      }
+      const match = await runnerColl.findOne();
+      debug('read metadata collection entry', insertedInfo, match);
+      if (!match) {
+        throw new Error(
+          'Cannot find mongodbrunner entry, assuming that this instance was not started by mongodb-runner',
+        );
+      }
+      if (match._id !== insertedInfo._id) {
+        throw new Error(
+          `Mismatched mongodbrunner entry: ${JSON.stringify(match)} !== ${JSON.stringify(insertedInfo)}`,
+        );
+      }
+    }
+  }
+
+  private async _populateBuildInfo(
+    mode: 'insert-new' | 'restore-check',
+  ): Promise<Error | null> {
+    try {
+      // directConnection + retryWrites let us write to `local` db on secondaries
+      const clientOpts = { retryWrites: false };
+      this.buildInfo = await this.withClient(async (client) => {
+        // Insert the metadata entry, except if we're a freshly started mongos
+        // (which does not have its own storage to persist)
+        await this._ensureMatchingMetadataColl(client, mode);
+        return await client.db('admin').command({ buildInfo: 1 });
+      }, clientOpts);
+    } catch (err) {
+      debug('failed to get buildInfo, treating as closed server', err);
+      return err as Error;
+    }
     debug(
       'got server build info through client',
       this.serverVersion,
       this.serverVariant,
     );
+    return null;
   }
 
   async withClient<Fn extends (client: MongoClient) => any>(
     fn: Fn,
+    clientOptions: MongoClientOptions = {},
   ): Promise<ReturnType<Fn>> {
-    const client = await MongoClient.connect(
-      `mongodb://${this.hostport}/?directConnection=true`,
-    );
+    const client = await MongoClient.connect(`mongodb://${this.hostport}/`, {
+      directConnection: true,
+      ...clientOptions,
+    });
     try {
       return await fn(client);
     } finally {
diff --git a/packages/mongodb-runner/src/runner-helpers.ts b/packages/mongodb-runner/src/runner-helpers.ts
index 4181b3eb..55c30913 100644
--- a/packages/mongodb-runner/src/runner-helpers.ts
+++ b/packages/mongodb-runner/src/runner-helpers.ts
@@ -84,14 +84,9 @@ export async function stop(argv: {
   id?: string;
   all?: boolean;
 }) {
-  const toStop: Array<StoredInstance> = [];
-  for await (const instance of instances(argv)) {
-    if (instance.id === argv.id || argv.all) toStop.push(instance);
-  }
-  await Promise.all(
-    toStop.map(async ({ filepath, serialized }) => {
-      await (await MongoCluster.deserialize(serialized)).close();
-      await fs.rm(filepath);
-    }),
-  );
+  await parallelForEach(instances(argv), async (instance: StoredInstance) => {
+    if (instance.id !== argv.id && !argv.all) return;
+    await (await MongoCluster.deserialize(instance.serialized)).close();
+    await fs.rm(instance.filepath);
+  });
 }
diff --git a/packages/mongodb-runner/src/util.ts b/packages/mongodb-runner/src/util.ts
index 8c1e36f6..bda4d3de 100644
--- a/packages/mongodb-runner/src/util.ts
+++ b/packages/mongodb-runner/src/util.ts
@@ -28,3 +28,16 @@ export async function parallelForEach<T>(
 
   return await Promise.allSettled(result);
 }
+
+export function pick<T extends object, K extends keyof T>(
+  obj: T,
+  keys: K[],
+): Pick<T, K> {
+  const ret: Partial<Pick<T, K>> = {};
+  for (const key of Object.keys(obj) as K[]) {
+    if (keys.includes(key)) {
+      ret[key] = obj[key];
+    }
+  }
+  return ret as Pick<T, K>;
+}