diff --git a/src/templates/template-repository.ts b/src/templates/template-repository.ts
index 696e449..c867800 100644
--- a/src/templates/template-repository.ts
+++ b/src/templates/template-repository.ts
@@ -625,22 +625,23 @@ export class TemplateRepository {
     
     return { total, withMetadata, withoutMetadata, outdated };
   }
-  
+
   /**
-   * Search templates by metadata fields
+   * Build WHERE conditions for metadata filtering
+   * @private
+   * @returns Object containing SQL conditions array and parameter values array
    */
-  searchTemplatesByMetadata(filters: {
+  private buildMetadataFilterConditions(filters: {
     category?: string;
     complexity?: 'simple' | 'medium' | 'complex';
     maxSetupMinutes?: number;
     minSetupMinutes?: number;
     requiredService?: string;
     targetAudience?: string;
-  }, limit: number = 20, offset: number = 0): StoredTemplate[] {
+  }): { conditions: string[], params: any[] } {
     const conditions: string[] = ['metadata_json IS NOT NULL'];
     const params: any[] = [];
 
-    // Build WHERE conditions based on filters with proper parameterization
     if (filters.category !== undefined) {
       // Use parameterized LIKE with JSON array search - safe from injection
       conditions.push("json_extract(metadata_json, '$.categories') LIKE '%' || ? || '%'");
@@ -680,34 +681,86 @@ export class TemplateRepository {
       params.push(sanitizedAudience);
     }
 
+    return { conditions, params };
+  }
+
+  /**
+   * Search templates by metadata fields
+   */
+  searchTemplatesByMetadata(filters: {
+    category?: string;
+    complexity?: 'simple' | 'medium' | 'complex';
+    maxSetupMinutes?: number;
+    minSetupMinutes?: number;
+    requiredService?: string;
+    targetAudience?: string;
+  }, limit: number = 20, offset: number = 0): StoredTemplate[] {
+    const startTime = Date.now();
+
+    // Build WHERE conditions using shared helper
+    const { conditions, params } = this.buildMetadataFilterConditions(filters);
+
     // Performance optimization: Use two-phase query to avoid loading large compressed workflows
     // during metadata filtering. This prevents timeout when no filters are provided.
     // Phase 1: Get IDs only with metadata filtering (fast - no workflow data)
+    // Add id to ORDER BY to ensure stable ordering
     const idsQuery = `
       SELECT id FROM templates
       WHERE ${conditions.join(' AND ')}
-      ORDER BY views DESC, created_at DESC
+      ORDER BY views DESC, created_at DESC, id ASC
       LIMIT ? OFFSET ?
     `;
 
     params.push(limit, offset);
     const ids = this.db.prepare(idsQuery).all(...params) as { id: number }[];
 
+    const phase1Time = Date.now() - startTime;
+
     if (ids.length === 0) {
-      logger.debug('Metadata search found 0 results', { filters });
+      logger.debug('Metadata search found 0 results', { filters, phase1Ms: phase1Time });
       return [];
     }
 
-    // Phase 2: Fetch full records only for matching IDs (only decompress needed rows)
-    const placeholders = ids.map(() => '?').join(',');
-    const fullQuery = `
-      SELECT * FROM templates
-      WHERE id IN (${placeholders})
-      ORDER BY views DESC, created_at DESC
-    `;
-    const results = this.db.prepare(fullQuery).all(...ids.map(r => r.id)) as StoredTemplate[];
+    // Defensive validation: ensure all IDs are valid positive integers
+    const idValues = ids.map(r => r.id).filter(id => typeof id === 'number' && id > 0 && Number.isInteger(id));
+
+    if (idValues.length === 0) {
+      logger.warn('No valid IDs after filtering', { filters, originalCount: ids.length });
+      return [];
+    }
+
+    if (idValues.length !== ids.length) {
+      logger.warn('Some IDs were filtered out as invalid', {
+        original: ids.length,
+        valid: idValues.length,
+        filtered: ids.length - idValues.length
+      });
+    }
+
+    // Phase 2: Fetch full records preserving exact order from Phase 1
+    // Use CTE with VALUES to maintain ordering without depending on SQLite's IN clause behavior
+    const phase2Start = Date.now();
+    const orderedQuery = `
+      WITH ordered_ids(id, sort_order) AS (
+        VALUES ${idValues.map((id, idx) => `(${id}, ${idx})`).join(', ')}
+      )
+      SELECT t.* FROM templates t
+      INNER JOIN ordered_ids o ON t.id = o.id
+      ORDER BY o.sort_order
+    `;
+
+    const results = this.db.prepare(orderedQuery).all() as StoredTemplate[];
+    const phase2Time = Date.now() - phase2Start;
+
+    logger.debug(`Metadata search found ${results.length} results`, {
+      filters,
+      count: results.length,
+      phase1Ms: phase1Time,
+      phase2Ms: phase2Time,
+      totalMs: Date.now() - startTime,
+      optimization: 'two-phase-with-ordering'
+    });
 
-    logger.debug(`Metadata search found ${results.length} results`, { filters, count: results.length });
     return results.map(t => this.decompressWorkflow(t));
   }
   
@@ -722,48 +775,12 @@ export class TemplateRepository {
     requiredService?: string;
     targetAudience?: string;
   }): number {
-    const conditions: string[] = ['metadata_json IS NOT NULL'];
-    const params: any[] = [];
-    
-    if (filters.category !== undefined) {
-      // Use parameterized LIKE with JSON array search - safe from injection
-      conditions.push("json_extract(metadata_json, '$.categories') LIKE '%' || ? || '%'");
-      const sanitizedCategory = JSON.stringify(filters.category).slice(1, -1);
-      params.push(sanitizedCategory);
-    }
-    
-    if (filters.complexity) {
-      conditions.push("json_extract(metadata_json, '$.complexity') = ?");
-      params.push(filters.complexity);
-    }
-    
-    if (filters.maxSetupMinutes !== undefined) {
-      conditions.push("CAST(json_extract(metadata_json, '$.estimated_setup_minutes') AS INTEGER) <= ?");
-      params.push(filters.maxSetupMinutes);
-    }
-    
-    if (filters.minSetupMinutes !== undefined) {
-      conditions.push("CAST(json_extract(metadata_json, '$.estimated_setup_minutes') AS INTEGER) >= ?");
-      params.push(filters.minSetupMinutes);
-    }
-    
-    if (filters.requiredService !== undefined) {
-      // Use parameterized LIKE with JSON array search - safe from injection
-      conditions.push("json_extract(metadata_json, '$.required_services') LIKE '%' || ? || '%'");
-      const sanitizedService = JSON.stringify(filters.requiredService).slice(1, -1);
-      params.push(sanitizedService);
-    }
-    
-    if (filters.targetAudience !== undefined) {
-      // Use parameterized LIKE with JSON array search - safe from injection
-      conditions.push("json_extract(metadata_json, '$.target_audience') LIKE '%' || ? || '%'");
-      const sanitizedAudience = JSON.stringify(filters.targetAudience).slice(1, -1);
-      params.push(sanitizedAudience);
-    }
-    
+    // Build WHERE conditions using shared helper
+    const { conditions, params } = this.buildMetadataFilterConditions(filters);
+
     const query = `SELECT COUNT(*) as count FROM templates WHERE ${conditions.join(' AND ')}`;
     const result = this.db.prepare(query).get(...params) as { count: number };
-    
+
     return result.count;
   }
   
diff --git a/tests/integration/database/template-repository.test.ts b/tests/integration/database/template-repository.test.ts
index bfac754..88b4849 100644
--- a/tests/integration/database/template-repository.test.ts
+++ b/tests/integration/database/template-repository.test.ts
@@ -643,6 +643,202 @@ describe('TemplateRepository Integration Tests', () => {
       });
     });
   });
+
+  describe('searchTemplatesByMetadata - Two-Phase Optimization', () => {
+  it('should use two-phase query pattern for performance', () => {
+    // Setup: Create templates with metadata
+    const templates = [
+      { id: 1, complexity: 'simple', category: 'automation' },
+      { id: 2, complexity: 'medium', category: 'integration' },
+      { id: 3, complexity: 'simple', category: 'automation' },
+      { id: 4, complexity: 'complex', category: 'data-processing' }
+    ];
+
+    templates.forEach(({ id, complexity, category }) => {
+      const template = createTemplateWorkflow({ id, name: `Template ${id}` });
+      const detail = createTemplateDetail({
+        id,
+        workflow: {
+          id: id.toString(),
+          name: `Template ${id}`,
+          nodes: [],
+          connections: {},
+          settings: {}
+        }
+      });
+
+      repository.saveTemplate(template, detail);
+
+      // Add metadata
+      const metadata = {
+        categories: [category],
+        complexity,
+        use_cases: ['test'],
+        estimated_setup_minutes: 15,
+        required_services: [],
+        key_features: ['test'],
+        target_audience: ['developers']
+      };
+
+      db.prepare(`
+        UPDATE templates
+        SET metadata_json = ?,
+            metadata_generated_at = datetime('now')
+        WHERE workflow_id = ?
+      `).run(JSON.stringify(metadata), id);
+    });
+
+    // Test: Search with filter should return matching templates
+    const results = repository.searchTemplatesByMetadata({ complexity: 'simple' }, 10, 0);
+
+    // Verify results
+    expect(results).toHaveLength(2);
+    expect(results[0].workflow_id).toBe(1); // Ordered by views DESC, then created_at DESC, then id ASC
+    expect(results[1].workflow_id).toBe(3);
+  });
+
+  it('should preserve exact ordering from Phase 1', () => {
+    // Setup: Create templates with different view counts
+    const templates = [
+      { id: 1, views: 100 },
+      { id: 2, views: 500 },
+      { id: 3, views: 300 },
+      { id: 4, views: 500 }, // Same views as id:2, should be ordered by id
+      { id: 5, views: 200 }
+    ];
+
+    templates.forEach(({ id, views }) => {
+      const template = createTemplateWorkflow({ id, name: `Template ${id}`, totalViews: views });
+      const detail = createTemplateDetail({
+        id,
+        views,
+        workflow: {
+          id: id.toString(),
+          name: `Template ${id}`,
+          nodes: [],
+          connections: {},
+          settings: {}
+        }
+      });
+
+      repository.saveTemplate(template, detail);
+
+      // Update views in database to match our test data
+      db.prepare(`UPDATE templates SET views = ? WHERE workflow_id = ?`).run(views, id);
+
+      // Add metadata
+      const metadata = {
+        categories: ['test'],
+        complexity: 'medium',
+        use_cases: ['test'],
+        estimated_setup_minutes: 15,
+        required_services: [],
+        key_features: ['test'],
+        target_audience: ['developers']
+      };
+
+      db.prepare(`
+        UPDATE templates
+        SET metadata_json = ?,
+            metadata_generated_at = datetime('now')
+        WHERE workflow_id = ?
+      `).run(JSON.stringify(metadata), id);
+    });
+
+    // Test: Search should return templates in correct order
+    const results = repository.searchTemplatesByMetadata({ complexity: 'medium' }, 10, 0);
+
+    // Verify ordering: 500 views (id 2), 500 views (id 4), 300 views, 200 views, 100 views
+    expect(results).toHaveLength(5);
+    expect(results[0].workflow_id).toBe(2); // 500 views, lower id
+    expect(results[1].workflow_id).toBe(4); // 500 views, higher id
+    expect(results[2].workflow_id).toBe(3); // 300 views
+    expect(results[3].workflow_id).toBe(5); // 200 views
+    expect(results[4].workflow_id).toBe(1); // 100 views
+  });
+
+  it('should handle empty results efficiently', () => {
+    // Setup: Create templates without the searched complexity
+    const template = createTemplateWorkflow({ id: 1 });
+    const detail = createTemplateDetail({
+      id: 1,
+      workflow: {
+        id: '1',
+        name: 'Template 1',
+        nodes: [],
+        connections: {},
+        settings: {}
+      }
+    });
+
+    repository.saveTemplate(template, detail);
+
+    const metadata = {
+      categories: ['test'],
+      complexity: 'simple',
+      use_cases: ['test'],
+      estimated_setup_minutes: 15,
+      required_services: [],
+      key_features: ['test'],
+      target_audience: ['developers']
+    };
+
+    db.prepare(`
+      UPDATE templates
+      SET metadata_json = ?,
+          metadata_generated_at = datetime('now')
+      WHERE workflow_id = 1
+    `).run(JSON.stringify(metadata));
+
+    // Test: Search for non-existent complexity
+    const results = repository.searchTemplatesByMetadata({ complexity: 'complex' }, 10, 0);
+
+    // Verify: Should return empty array without errors
+    expect(results).toHaveLength(0);
+  });
+
+  it('should validate IDs defensively', () => {
+    // This test ensures the defensive ID validation works
+    // Setup: Create a template
+    const template = createTemplateWorkflow({ id: 1 });
+    const detail = createTemplateDetail({
+      id: 1,
+      workflow: {
+        id: '1',
+        name: 'Template 1',
+        nodes: [],
+        connections: {},
+        settings: {}
+      }
+    });
+
+    repository.saveTemplate(template, detail);
+
+    const metadata = {
+      categories: ['test'],
+      complexity: 'simple',
+      use_cases: ['test'],
+      estimated_setup_minutes: 15,
+      required_services: [],
+      key_features: ['test'],
+      target_audience: ['developers']
+    };
+
+    db.prepare(`
+      UPDATE templates
+      SET metadata_json = ?,
+          metadata_generated_at = datetime('now')
+      WHERE workflow_id = 1
+    `).run(JSON.stringify(metadata));
+
+    // Test: Normal search should work
+    const results = repository.searchTemplatesByMetadata({ complexity: 'simple' }, 10, 0);
+
+    // Verify: Should return the template
+    expect(results).toHaveLength(1);
+    expect(results[0].workflow_id).toBe(1);
+  });
+  });
 });
 
 // Helper functions