mongodb-js · kmruiz · Jun 26, 2025 · Jun 18, 2025 · Jun 20, 2025 · Jun 20, 2025
@@ -24,11 +24,17 @@ startCommand:
         title: Read-only
         description: When set to true, only allows read and metadata operation types, disabling create/update/delete operations.
         default: false
+      indexCheck:
+        type: boolean
+        title: Index Check
+        description: When set to true, enforces that query operations must use an index, rejecting queries that would perform a collection scan.
+        default: false
   exampleConfig:
     atlasClientId: YOUR_ATLAS_CLIENT_ID
     atlasClientSecret: YOUR_ATLAS_CLIENT_SECRET
     connectionString: mongodb+srv://USERNAME:PASSWORD@YOUR_CLUSTER.mongodb.net
     readOnly: true
+    indexCheck: false
 
   commandFunction:
     # A function that produces the CLI command to start the MCP on stdio.
@@ -54,6 +60,10 @@ startCommand:
           args.push('--connectionString');
           args.push(config.connectionString);
         }
+
+        if (config.indexCheck) {
+          args.push('--indexCheck');
+        }
       }
 
       return {

@@ -267,6 +267,7 @@ The MongoDB MCP Server can be configured using multiple methods, with the follow
 | `logPath`          | Folder to store logs.                                                                                                                                         |
 | `disabledTools`    | An array of tool names, operation types, and/or categories of tools that will be disabled.                                                                    |
 | `readOnly`         | When set to true, only allows read and metadata operation types, disabling create/update/delete operations.                                                   |
+| `indexCheck`       | When set to true, enforces that query operations must use an index, rejecting queries that perform a collection scan.                                         |
 | `telemetry`        | When set to disabled, disables telemetry collection.                                                                                                          |
 
 #### Log Path
@@ -312,6 +313,19 @@ You can enable read-only mode using:
 
 When read-only mode is active, you'll see a message in the server logs indicating which tools were prevented from registering due to this restriction.
 
+#### Index Check Mode
+
+The `indexCheck` configuration option allows you to enforce that query operations must use an index. When enabled, queries that perform a collection scan will be rejected to ensure better performance.
+
+This is useful for scenarios where you want to ensure that database queries are optimized.
+
+You can enable index check mode using:
+
+- **Environment variable**: `export MDB_MCP_INDEX_CHECK=true`
+- **Command-line argument**: `--indexCheck`
+
+When index check mode is active, you'll see an error message if a query is rejected due to not using an index.
+
 #### Telemetry
 
 The `telemetry` configuration option allows you to disable telemetry collection. When enabled, the MCP server will collect usage data and send it to MongoDB.
@@ -430,7 +444,7 @@ export MDB_MCP_LOG_PATH="/path/to/logs"
 Pass configuration options as command-line arguments when starting the server:
 
 ```shell
-npx -y mongodb-mcp-server --apiClientId="your-atlas-service-accounts-client-id" --apiClientSecret="your-atlas-service-accounts-client-secret" --connectionString="mongodb+srv://username:password@cluster.mongodb.net/myDatabase" --logPath=/path/to/logs
+npx -y mongodb-mcp-server --apiClientId="your-atlas-service-accounts-client-id" --apiClientSecret="your-atlas-service-accounts-client-secret" --connectionString="mongodb+srv://username:password@cluster.mongodb.net/myDatabase" --logPath=/path/to/logs --readOnly --indexCheck
 ```
 
 #### MCP configuration file examples

@@ -23,6 +23,7 @@ export interface UserConfig {
     connectOptions: ConnectOptions;
     disabledTools: Array<string>;
     readOnly?: boolean;
+    indexCheck?: boolean;
 }
 
 const defaults: UserConfig = {
@@ -37,6 +38,7 @@ const defaults: UserConfig = {
     disabledTools: [],
     telemetry: "enabled",
     readOnly: false,
+    indexCheck: false,
 };
 
 export const config = {

@@ -1,6 +1,7 @@
 export enum ErrorCodes {
     NotConnectedToMongoDB = 1_000_000,
     MisconfiguredConnectionString = 1_000_001,
+    ForbiddenCollscan = 1_000_002,
 }
 
 export class MongoDBError extends Error {

@@ -0,0 +1,83 @@
+import { Document } from "mongodb";
+import { NodeDriverServiceProvider } from "@mongosh/service-provider-node-driver";
+import { ErrorCodes, MongoDBError } from "../errors.js";
+
+/**
+ * Check if the query plan uses an index
+ * @param explainResult The result of the explain query
+ * @returns true if an index is used, false if it's a full collection scan
+ */
+export function usesIndex(explainResult: Document): boolean {
+    const queryPlanner = explainResult?.queryPlanner as Document | undefined;
+    const winningPlan = queryPlanner?.winningPlan as Document | undefined;
+    const stage = winningPlan?.stage as string | undefined;
+    const inputStage = winningPlan?.inputStage as Document | undefined;
+
+    // Check for index scan stages (including MongoDB 8.0+ stages)
+    const indexScanStages = [
+        "IXSCAN",
+        "COUNT_SCAN",
+        "EXPRESS_IXSCAN",
+        "EXPRESS_CLUSTERED_IXSCAN",
+        "EXPRESS_UPDATE",
+        "EXPRESS_DELETE",
+        "IDHACK",
+    ];
+
+    if (stage && indexScanStages.includes(stage)) {
+        return true;
+    }
+
+    if (inputStage && inputStage.stage && indexScanStages.includes(inputStage.stage as string)) {
+        return true;
+    }
+
+    // Recursively check deeper stages
+    if (inputStage && inputStage.inputStage) {
+        return usesIndex({ queryPlanner: { winningPlan: inputStage } });
+    }
+
+    if (stage === "COLLSCAN") {
+        return false;
+    }
+
+    // Default to false (conservative approach)
+    return false;
+}
+
+/**
+ * Generate an error message for index check failure
+ */
+export function getIndexCheckErrorMessage(database: string, collection: string, operation: string): string {
+    return `Index check failed: The ${operation} operation on "${database}.${collection}" performs a collection scan (COLLSCAN) instead of using an index. Consider adding an index for better performance. Use 'explain' tool for query plan analysis or 'collection-indexes' to view existing indexes. To disable this check, set MDB_MCP_INDEX_CHECK to false.`;
+}
+
+/**
+ * Generic function to perform index usage check
+ */
+export async function checkIndexUsage(
+    provider: NodeDriverServiceProvider,
+    database: string,
+    collection: string,
+    operation: string,
+    explainCallback: () => Promise<Document>
+): Promise<void> {
+    try {
+        const explainResult = await explainCallback();
+
+        if (!usesIndex(explainResult)) {
+            throw new MongoDBError(
+                ErrorCodes.ForbiddenCollscan,
+                getIndexCheckErrorMessage(database, collection, operation)
+            );
+        }
+    } catch (error) {
+        if (error instanceof MongoDBError && error.code === ErrorCodes.ForbiddenCollscan) {
+            throw error;
+        }
+
+        // If explain itself fails, log but do not prevent query execution
+        // This avoids blocking normal queries in special cases (e.g., permission issues)
+        console.warn(`Index check failed to execute explain for ${operation} on ${database}.${collection}:`, error);
+    }
+}
@@ -2,6 +2,7 @@ import { z } from "zod";
 import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
+import { checkIndexUsage } from "../../../helpers/indexCheck.js";
 
 export class DeleteManyTool extends MongoDBToolBase {
     protected name = "delete-many";
@@ -23,6 +24,25 @@ export class DeleteManyTool extends MongoDBToolBase {
         filter,
     }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
+
+        // Check if delete operation uses an index if enabled
+        if (this.config.indexCheck) {
+            await checkIndexUsage(provider, database, collection, "deleteMany", async () => {
+                return provider.runCommandWithCheck(database, {
+                    explain: {
+                        delete: collection,
+                        deletes: [
+                            {
+                                q: filter || {},
+                                limit: 0, // 0 means delete all matching documents
+                            },
+                        ],
+                    },
+                    verbosity: "queryPlanner",
+                });
+            });
+        }
+
         const result = await provider.deleteMany(database, collection, filter);
 
         return {

@@ -76,7 +76,7 @@ export class ExplainTool extends MongoDBToolBase {
             }
             case "count": {
                 const { query } = method.arguments;
-                result = await provider.mongoClient.db(database).command({
+                result = await provider.runCommandWithCheck(database, {
                     explain: {
                         count: collection,
                         query,

@@ -64,6 +64,16 @@ export abstract class MongoDBToolBase extends ToolBase {
                         ],
                         isError: true,
                     };
+                case ErrorCodes.ForbiddenCollscan:
+                    return {
+                        content: [
+                            {
+                                type: "text",
+                                text: error.message,
+                            },
+                        ],
+                        isError: true,
+                    };
             }
         }
 

@@ -3,6 +3,7 @@ import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
 import { EJSON } from "bson";
+import { checkIndexUsage } from "../../../helpers/indexCheck.js";
 
 export const AggregateArgs = {
     pipeline: z.array(z.record(z.string(), z.unknown())).describe("An array of aggregation stages to execute"),
@@ -23,6 +24,16 @@ export class AggregateTool extends MongoDBToolBase {
         pipeline,
     }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
+
+        // Check if aggregate operation uses an index if enabled
+        if (this.config.indexCheck) {
+            await checkIndexUsage(provider, database, collection, "aggregate", async () => {
+                return provider
+                    .aggregate(database, collection, pipeline, {}, { writeConcern: undefined })
+                    .explain("queryPlanner");
+            });
+        }
+
         const documents = await provider.aggregate(database, collection, pipeline).toArray();
 
         const content: Array<{ text: string; type: "text" }> = [

@@ -2,6 +2,7 @@ import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
 import { z } from "zod";
+import { checkIndexUsage } from "../../../helpers/indexCheck.js";
 
 export const CountArgs = {
     query: z
@@ -25,6 +26,20 @@ export class CountTool extends MongoDBToolBase {
 
     protected async execute({ database, collection, query }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
+
+        // Check if count operation uses an index if enabled
+        if (this.config.indexCheck) {
+            await checkIndexUsage(provider, database, collection, "count", async () => {
+                return provider.runCommandWithCheck(database, {
+                    explain: {
+                        count: collection,
+                        query,
+                    },
+                    verbosity: "queryPlanner",
+                });
+            });
+        }
+
         const count = await provider.count(database, collection, query);
 
         return {

@@ -4,6 +4,7 @@ import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
 import { SortDirection } from "mongodb";
 import { EJSON } from "bson";
+import { checkIndexUsage } from "../../../helpers/indexCheck.js";
 
 export const FindArgs = {
     filter: z
@@ -39,6 +40,14 @@ export class FindTool extends MongoDBToolBase {
         sort,
     }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
+
+        // Check if find operation uses an index if enabled
+        if (this.config.indexCheck) {
+            await checkIndexUsage(provider, database, collection, "find", async () => {
+                return provider.find(database, collection, filter, { projection, limit, sort }).explain("queryPlanner");
+            });
+        }
+
         const documents = await provider.find(database, collection, filter, { projection, limit, sort }).toArray();
 
         const content: Array<{ text: string; type: "text" }> = [

@@ -2,6 +2,7 @@ import { z } from "zod";
 import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
+import { checkIndexUsage } from "../../../helpers/indexCheck.js";
 
 export class UpdateManyTool extends MongoDBToolBase {
     protected name = "update-many";
@@ -32,6 +33,27 @@ export class UpdateManyTool extends MongoDBToolBase {
         upsert,
     }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
+
+        // Check if update operation uses an index if enabled
+        if (this.config.indexCheck) {
+            await checkIndexUsage(provider, database, collection, "updateMany", async () => {
+                return provider.runCommandWithCheck(database, {
+                    explain: {
+                        update: collection,
+                        updates: [
+                            {
+                                q: filter || {},
+                                u: update,
+                                upsert: upsert || false,
+                                multi: true,
+                            },
+                        ],
+                    },
+                    verbosity: "queryPlanner",
+                });
+            });
+        }
+
         const result = await provider.updateMany(database, collection, filter, update, {
             upsert,
         });