diff --git a/tests/benchmarks/database-queries.bench.ts b/tests/benchmarks/database-queries.bench.ts
index 99d20a7..481c403 100644
--- a/tests/benchmarks/database-queries.bench.ts
+++ b/tests/benchmarks/database-queries.bench.ts
@@ -4,6 +4,17 @@ import { SQLiteStorageService } from '../../src/services/sqlite-storage-service'
 import { NodeFactory } from '../factories/node-factory';
 import { PropertyDefinitionFactory } from '../factories/property-definition-factory';
 
+/**
+ * Database Query Performance Benchmarks
+ *
+ * NOTE: These benchmarks use MOCK DATA (500 artificial test nodes)
+ * created with factories, not the real production database.
+ *
+ * This is useful for tracking database layer performance in isolation,
+ * but may not reflect real-world performance characteristics.
+ *
+ * For end-to-end MCP tool performance with real data, see mcp-tools.bench.ts
+ */
 describe('Database Query Performance', () => {
   let repository: NodeRepository;
   let storage: SQLiteStorageService;
diff --git a/tests/benchmarks/index.ts b/tests/benchmarks/index.ts
index 05b5802..8adb81c 100644
--- a/tests/benchmarks/index.ts
+++ b/tests/benchmarks/index.ts
@@ -1,7 +1,3 @@
 // Export all benchmark suites
-// Note: Some benchmarks are temporarily disabled due to API changes
-// export * from './node-loading.bench';
 export * from './database-queries.bench';
-// export * from './search-operations.bench';
-// export * from './validation-performance.bench';
-// export * from './mcp-tools.bench';
\ No newline at end of file
+export * from './mcp-tools.bench';
\ No newline at end of file
diff --git a/tests/benchmarks/mcp-tools.bench.ts b/tests/benchmarks/mcp-tools.bench.ts
new file mode 100644
index 0000000..c4a527a
--- /dev/null
+++ b/tests/benchmarks/mcp-tools.bench.ts
@@ -0,0 +1,169 @@
+import { bench, describe } from 'vitest';
+import { NodeRepository } from '../../src/database/node-repository';
+import { createDatabaseAdapter } from '../../src/database/database-adapter';
+import { EnhancedConfigValidator } from '../../src/services/enhanced-config-validator';
+import { PropertyFilter } from '../../src/services/property-filter';
+import path from 'path';
+
+/**
+ * MCP Tool Performance Benchmarks
+ *
+ * These benchmarks measure end-to-end performance of actual MCP tool operations
+ * using the REAL production database (data/nodes.db with 525+ nodes).
+ *
+ * Unlike database-queries.bench.ts which uses mock data, these benchmarks
+ * reflect what AI assistants actually experience when calling MCP tools,
+ * making this the most meaningful performance metric for the system.
+ */
+describe('MCP Tool Performance (Production Database)', () => {
+  let repository: NodeRepository;
+
+  beforeAll(async () => {
+    // Use REAL production database
+    const dbPath = path.join(__dirname, '../../data/nodes.db');
+    const db = await createDatabaseAdapter(dbPath);
+    repository = new NodeRepository(db);
+    // Initialize similarity services for validation
+    EnhancedConfigValidator.initializeSimilarityServices(repository);
+  });
+
+  /**
+   * search_nodes - Most frequently used tool for node discovery
+   *
+   * This measures:
+   * - Database FTS5 full-text search
+   * - Result filtering and ranking
+   * - Response serialization
+   *
+   * Target: <20ms for common queries
+   */
+  bench('search_nodes - common query (http)', async () => {
+    await repository.searchNodes('http', 'OR', 20);
+  }, {
+    iterations: 100,
+    warmupIterations: 10,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  bench('search_nodes - AI agent query (slack message)', async () => {
+    await repository.searchNodes('slack send message', 'AND', 10);
+  }, {
+    iterations: 100,
+    warmupIterations: 10,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  /**
+   * get_node_essentials - Fast retrieval of node configuration
+   *
+   * This measures:
+   * - Database node lookup
+   * - Property filtering (essentials only)
+   * - Response formatting
+   *
+   * Target: <10ms for most nodes
+   */
+  bench('get_node_essentials - HTTP Request node', async () => {
+    const node = await repository.getNodeByType('n8n-nodes-base.httpRequest');
+    if (node && node.properties) {
+      PropertyFilter.getEssentials(node.properties, node.nodeType);
+    }
+  }, {
+    iterations: 200,
+    warmupIterations: 20,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  bench('get_node_essentials - Slack node', async () => {
+    const node = await repository.getNodeByType('n8n-nodes-base.slack');
+    if (node && node.properties) {
+      PropertyFilter.getEssentials(node.properties, node.nodeType);
+    }
+  }, {
+    iterations: 200,
+    warmupIterations: 20,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  /**
+   * list_nodes - Initial exploration/listing
+   *
+   * This measures:
+   * - Database query with pagination
+   * - Result serialization
+   * - Category filtering
+   *
+   * Target: <15ms for first page
+   */
+  bench('list_nodes - first 50 nodes', async () => {
+    await repository.getAllNodes(50);
+  }, {
+    iterations: 100,
+    warmupIterations: 10,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  bench('list_nodes - AI tools only', async () => {
+    await repository.getAIToolNodes();
+  }, {
+    iterations: 100,
+    warmupIterations: 10,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  /**
+   * validate_node_operation - Configuration validation
+   *
+   * This measures:
+   * - Schema lookup
+   * - Validation logic execution
+   * - Error message formatting
+   *
+   * Target: <15ms for simple validations
+   */
+  bench('validate_node_operation - HTTP Request (minimal)', async () => {
+    const node = await repository.getNodeByType('n8n-nodes-base.httpRequest');
+    if (node && node.properties) {
+      EnhancedConfigValidator.validateWithMode(
+        'n8n-nodes-base.httpRequest',
+        {},
+        node.properties,
+        'operation',
+        'ai-friendly'
+      );
+    }
+  }, {
+    iterations: 100,
+    warmupIterations: 10,
+    warmupTime: 500,
+    time: 3000
+  });
+
+  bench('validate_node_operation - HTTP Request (with params)', async () => {
+    const node = await repository.getNodeByType('n8n-nodes-base.httpRequest');
+    if (node && node.properties) {
+      EnhancedConfigValidator.validateWithMode(
+        'n8n-nodes-base.httpRequest',
+        {
+          requestMethod: 'GET',
+          url: 'https://api.example.com',
+          authentication: 'none'
+        },
+        node.properties,
+        'operation',
+        'ai-friendly'
+      );
+    }
+  }, {
+    iterations: 100,
+    warmupIterations: 10,
+    warmupTime: 500,
+    time: 3000
+  });
+});
diff --git a/tests/benchmarks/sample.bench.ts b/tests/benchmarks/sample.bench.ts
deleted file mode 100644
index 2b2451a..0000000
--- a/tests/benchmarks/sample.bench.ts
+++ /dev/null
@@ -1,47 +0,0 @@
-import { bench, describe } from 'vitest';
-
-/**
- * Sample benchmark to verify the setup works correctly
- */
-describe('Sample Benchmarks', () => {
-  bench('array sorting - small', () => {
-    const arr = Array.from({ length: 100 }, () => Math.random());
-    arr.sort((a, b) => a - b);
-  }, {
-    iterations: 1000,
-    warmupIterations: 100
-  });
-
-  bench('array sorting - large', () => {
-    const arr = Array.from({ length: 10000 }, () => Math.random());
-    arr.sort((a, b) => a - b);
-  }, {
-    iterations: 100,
-    warmupIterations: 10
-  });
-
-  bench('string concatenation', () => {
-    let str = '';
-    for (let i = 0; i < 1000; i++) {
-      str += 'a';
-    }
-  }, {
-    iterations: 1000,
-    warmupIterations: 100
-  });
-
-  bench('object creation', () => {
-    const objects = [];
-    for (let i = 0; i < 1000; i++) {
-      objects.push({
-        id: i,
-        name: `Object ${i}`,
-        value: Math.random(),
-        timestamp: Date.now()
-      });
-    }
-  }, {
-    iterations: 1000,
-    warmupIterations: 100
-  });
-});
\ No newline at end of file