diff --git a/.changeset/mongo-objectid-normalize.md b/.changeset/mongo-objectid-normalize.md
new file mode 100644
index 0000000000..124e62d12a
--- /dev/null
+++ b/.changeset/mongo-objectid-normalize.md
@@ -0,0 +1,5 @@
+---
+"@better-auth/mongo-adapter": patch
+---
+
+Recognize ObjectId and UUID values returned by a `mongodb` driver that loaded a different `bson` module instance, so ids are normalized to strings instead of failing `instanceof`.
diff --git a/packages/mongo-adapter/src/mongodb-adapter.test.ts b/packages/mongo-adapter/src/mongodb-adapter.test.ts
index 5142aa33d2..1d6ba53509 100644
--- a/packages/mongo-adapter/src/mongodb-adapter.test.ts
+++ b/packages/mongo-adapter/src/mongodb-adapter.test.ts
@@ -1,3 +1,4 @@
+import type { BetterAuthOptions } from "@better-auth/core";
 import type { Db } from "mongodb";
 import { ObjectId, UUID } from "mongodb";
 import { describe, expect, it, vi } from "vitest";
@@ -535,3 +536,74 @@ describe("uuid support", () => {
 		expect((result as Record<string, unknown>).id).toBe(uuid);
 	});
 });
+
+/**
+ * When the driver and the adapter resolve different `bson` module instances
+ * (CJS vs ESM entry point), driver values fail `instanceof` against the
+ * adapter's classes and must be recognized structurally instead.
+ * @see https://github.com/better-auth/better-auth/issues/11065
+ */
+describe("ids from a different bson instance", () => {
+	const hex = "000000000000000000000001";
+	const uuid = "550e8400-e29b-41d4-a716-446655440000";
+	const foreignObjectId = { _bsontype: "ObjectId", toHexString: () => hex };
+	const foreignUUID = {
+		_bsontype: "Binary",
+		sub_type: 4,
+		toHexString: () => uuid,
+		toString: () => uuid,
+	};
+
+	function createAdapterReturning(
+		document: Record<string, unknown>,
+		generateId?: "uuid",
+	) {
+		const aggregate = vi.fn(() => ({
+			toArray: vi.fn(async () => [document]),
+		}));
+		const db = { collection: vi.fn(() => ({ aggregate })) } as unknown as Db;
+		const adapter = mongodbAdapter(db, { transaction: false })({
+			advanced: { database: generateId ? { generateId } : {} },
+		} as unknown as BetterAuthOptions);
+		return { adapter, aggregate };
+	}
+
+	it("normalizes a foreign ObjectId to its hex string", async () => {
+		const { adapter } = createAdapterReturning({
+			_id: foreignObjectId,
+			email: "example@example.test",
+		});
+		const user = await adapter.findOne<{ id: unknown }>({
+			model: "user",
+			where: [],
+		});
+		expect(user?.id).toBe(hex);
+	});
+
+	it("normalizes a foreign UUID to its string form", async () => {
+		const { adapter } = createAdapterReturning(
+			{ _id: foreignUUID, email: "example@example.test" },
+			"uuid",
+		);
+		const user = await adapter.findOne<{ id: unknown }>({
+			model: "user",
+			where: [],
+		});
+		expect(user?.id).toBe(uuid);
+	});
+
+	it("accepts a foreign ObjectId as a where clause value", async () => {
+		const { adapter, aggregate } = createAdapterReturning({
+			_id: foreignObjectId,
+			email: "example@example.test",
+		});
+		await adapter.findOne({
+			model: "user",
+			where: [{ field: "id", value: foreignObjectId as unknown as string }],
+		});
+		expect(aggregate).toHaveBeenCalledWith(
+			expect.arrayContaining([{ $match: { _id: foreignObjectId } }]),
+			expect.anything(),
+		);
+	});
+});
diff --git a/packages/mongo-adapter/src/mongodb-adapter.ts b/packages/mongo-adapter/src/mongodb-adapter.ts
index b70c58d474..e2b9606ccc 100644
--- a/packages/mongo-adapter/src/mongodb-adapter.ts
+++ b/packages/mongo-adapter/src/mongodb-adapter.ts
@@ -21,6 +21,32 @@ import {
 	insensitiveStartsWith,
 } from "./query-builders";
 
+/**
+ * Structural checks for BSON ids. The driver may resolve a different `bson`
+ * module instance than the adapter (CJS vs ESM entry point), in which case
+ * its values fail `instanceof` against the adapter's classes.
+ * @see https://github.com/better-auth/better-auth/issues/11065
+ */
+function isObjectIdLike(value: unknown): value is ObjectId {
+	if (typeof value !== "object" || value === null) return false;
+	const { _bsontype, toHexString } = value as Record<string, unknown>;
+	return (
+		(_bsontype === "ObjectId" || _bsontype === "ObjectID") &&
+		typeof toHexString === "function"
+	);
+}
+
+function isUUIDLike(value: unknown): value is UUID {
+	if (typeof value !== "object" || value === null) return false;
+	const { _bsontype, sub_type, toHexString } = value as Record<string, unknown>;
+	// A BSON UUID is a Binary with sub_type 4.
+	return (
+		_bsontype === "Binary" &&
+		sub_type === 4 &&
+		typeof toHexString === "function"
+	);
+}
+
 class MongoAdapterError extends Error {
 	constructor(
 		public code: "INVALID_ID" | "UNSUPPORTED_OPERATOR",
@@ -157,8 +183,8 @@ export const mongodbAdapter = (
 			}
 
 			function isIdInstance(value: unknown): value is ObjectId | UUID {
-				if (useUUIDs) return value instanceof UUID;
-				return value instanceof ObjectId;
+				if (useUUIDs) return isUUIDLike(value);
+				return isObjectIdLike(value);
 			}
 
 			function serializeID({
@@ -801,9 +827,9 @@ export const mongodbAdapter = (
 					if (action !== "create" && action !== "update") {
 						return data;
 					}
-					const IdClass =
-						options.advanced?.database?.generateId === "uuid" ? UUID : ObjectId;
-					if (data instanceof IdClass) {
+					const useUUIDs = options.advanced?.database?.generateId === "uuid";
+					const IdClass = useUUIDs ? UUID : ObjectId;
+					if (useUUIDs ? isUUIDLike(data) : isObjectIdLike(data)) {
 						return data;
 					}
 					if (Array.isArray(data)) {
@@ -841,18 +867,18 @@ export const mongodbAdapter = (
 			},
 			customTransformOutput({ data, field, fieldAttributes }) {
 				if (field === "id" || fieldAttributes.references?.field === "id") {
-					if (data instanceof UUID) {
+					if (isUUIDLike(data)) {
 						return data.toString();
 					}
-					if (data instanceof ObjectId) {
+					if (isObjectIdLike(data)) {
 						return data.toHexString();
 					}
 					if (Array.isArray(data)) {
 						return data.map((v) => {
-							if (v instanceof UUID) {
+							if (isUUIDLike(v)) {
 								return v.toString();
 							}
-							if (v instanceof ObjectId) {
+							if (isObjectIdLike(v)) {
 								return v.toHexString();
 							}
 							return v;