diff --git a/src/services/code-index/__tests__/service-factory.spec.ts b/src/services/code-index/__tests__/service-factory.spec.ts
index 1d8f7ba4786..ae229077d25 100644
--- a/src/services/code-index/__tests__/service-factory.spec.ts
+++ b/src/services/code-index/__tests__/service-factory.spec.ts
@@ -345,6 +345,125 @@ describe("CodeIndexServiceFactory", () => {
 			mockGetDefaultModelId.mockReturnValue("default-model")
 		})
 
+		it("should prioritize detectedDimension over all other dimension sources", () => {
+			// Arrange
+			const testConfig = {
+				embedderProvider: "openai-compatible",
+				modelId: "custom-model",
+				modelDimension: 1024, // Manual config should be ignored
+				qdrantUrl: "http://localhost:6333",
+				qdrantApiKey: "test-key",
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			mockGetModelDimension.mockReturnValue(768) // Profile dimension should be ignored
+
+			// Act - pass detected dimension from validation
+			factory.createVectorStore(4096)
+
+			// Assert - should use detected dimension (4096), not profile (768) or manual (1024)
+			expect(MockedQdrantVectorStore).toHaveBeenCalledWith(
+				"/test/workspace",
+				"http://localhost:6333",
+				4096, // Auto-detected dimension takes priority
+				"test-key",
+			)
+		})
+
+		it("should use detected dimension from Ollama embedder", () => {
+			// Arrange - simulates Ollama with qwen3-embedding returning 4096 dimensions
+			const testConfig = {
+				embedderProvider: "ollama",
+				modelId: "qwen3-embedding",
+				modelDimension: 1536, // User's incorrect manual config
+				qdrantUrl: "http://localhost:6333",
+				qdrantApiKey: "test-key",
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			mockGetModelDimension.mockReturnValue(undefined) // Unknown model
+
+			// Act - pass detected dimension from validation (like the issue scenario)
+			factory.createVectorStore(4096)
+
+			// Assert - should use auto-detected 4096, not user's incorrect 1536
+			expect(MockedQdrantVectorStore).toHaveBeenCalledWith(
+				"/test/workspace",
+				"http://localhost:6333",
+				4096,
+				"test-key",
+			)
+		})
+
+		it("should fall back to profile dimension when detected dimension is not provided", () => {
+			// Arrange
+			const testConfig = {
+				embedderProvider: "openai",
+				modelId: "text-embedding-3-large",
+				qdrantUrl: "http://localhost:6333",
+				qdrantApiKey: "test-key",
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			mockGetModelDimension.mockReturnValue(3072)
+
+			// Act - no detected dimension provided
+			factory.createVectorStore()
+
+			// Assert - should use profile dimension
+			expect(mockGetModelDimension).toHaveBeenCalledWith("openai", "text-embedding-3-large")
+			expect(MockedQdrantVectorStore).toHaveBeenCalledWith(
+				"/test/workspace",
+				"http://localhost:6333",
+				3072,
+				"test-key",
+			)
+		})
+
+		it("should fall back to manual dimension when detected and profile are unavailable", () => {
+			// Arrange
+			const testConfig = {
+				embedderProvider: "openai-compatible",
+				modelId: "unknown-model",
+				modelDimension: 2048,
+				qdrantUrl: "http://localhost:6333",
+				qdrantApiKey: "test-key",
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			mockGetModelDimension.mockReturnValue(undefined)
+
+			// Act - no detected dimension, no profile dimension
+			factory.createVectorStore()
+
+			// Assert - should use manual dimension
+			expect(MockedQdrantVectorStore).toHaveBeenCalledWith(
+				"/test/workspace",
+				"http://localhost:6333",
+				2048,
+				"test-key",
+			)
+		})
+
+		it("should ignore zero or negative detected dimension", () => {
+			// Arrange
+			const testConfig = {
+				embedderProvider: "openai",
+				modelId: "text-embedding-3-small",
+				qdrantUrl: "http://localhost:6333",
+				qdrantApiKey: "test-key",
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			mockGetModelDimension.mockReturnValue(1536)
+
+			// Act - pass invalid detected dimension
+			factory.createVectorStore(0)
+
+			// Assert - should fall back to profile dimension
+			expect(MockedQdrantVectorStore).toHaveBeenCalledWith(
+				"/test/workspace",
+				"http://localhost:6333",
+				1536,
+				"test-key",
+			)
+		})
+
 		it("should use config.modelId for OpenAI provider", () => {
 			// Arrange
 			const testModelId = "text-embedding-3-large"
@@ -670,6 +789,58 @@ describe("CodeIndexServiceFactory", () => {
 			}
 		})
 
+		it("should return detectedDimension from embedder validation", async () => {
+			// Arrange
+			const testConfig = {
+				embedderProvider: "ollama",
+				modelId: "qwen3-embedding",
+				ollamaOptions: {
+					ollamaBaseUrl: "http://localhost:11434",
+				},
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			MockedCodeIndexOllamaEmbedder.mockImplementation(() => mockEmbedderInstance)
+			// Mock embedder returning detected dimension
+			mockEmbedderInstance.validateConfiguration.mockResolvedValue({
+				valid: true,
+				detectedDimension: 4096,
+			})
+
+			// Act
+			const embedder = factory.createEmbedder()
+			const result = await factory.validateEmbedder(embedder)
+
+			// Assert
+			expect(result).toEqual({ valid: true, detectedDimension: 4096 })
+			expect(mockEmbedderInstance.validateConfiguration).toHaveBeenCalled()
+		})
+
+		it("should return detectedDimension from base64 embedding validation", async () => {
+			// Arrange
+			const testConfig = {
+				embedderProvider: "openai-compatible",
+				modelId: "custom-model",
+				openAiCompatibleOptions: {
+					baseUrl: "https://api.example.com/v1",
+					apiKey: "test-api-key",
+				},
+			}
+			mockConfigManager.getConfig.mockReturnValue(testConfig as any)
+			MockedOpenAICompatibleEmbedder.mockImplementation(() => mockEmbedderInstance)
+			// Mock embedder returning detected dimension from base64 parsing
+			mockEmbedderInstance.validateConfiguration.mockResolvedValue({
+				valid: true,
+				detectedDimension: 1536,
+			})
+
+			// Act
+			const embedder = factory.createEmbedder()
+			const result = await factory.validateEmbedder(embedder)
+
+			// Assert
+			expect(result).toEqual({ valid: true, detectedDimension: 1536 })
+		})
+
 		it("should validate OpenAI embedder successfully", async () => {
 			// Arrange
 			const testConfig = {
diff --git a/src/services/code-index/embedders/__tests__/ollama.spec.ts b/src/services/code-index/embedders/__tests__/ollama.spec.ts
index 650140beacf..4b9dffaeb1b 100644
--- a/src/services/code-index/embedders/__tests__/ollama.spec.ts
+++ b/src/services/code-index/embedders/__tests__/ollama.spec.ts
@@ -196,6 +196,7 @@ describe("CodeIndexOllamaEmbedder", () => {
 
 			expect(result.valid).toBe(true)
 			expect(result.error).toBeUndefined()
+			expect(result.detectedDimension).toBe(3) // Auto-detected from test embedding
 			expect(mockFetch).toHaveBeenCalledTimes(2)
 
 			// Check first call (GET /api/tags)
@@ -214,6 +215,38 @@ describe("CodeIndexOllamaEmbedder", () => {
 			expect(secondCall[1]?.signal).toBeDefined() // AbortSignal for timeout
 		})
 
+		it("should detect dimension from realistic embedding size", async () => {
+			// Mock successful /api/tags call
+			mockFetch.mockImplementationOnce(() =>
+				Promise.resolve({
+					ok: true,
+					status: 200,
+					json: () =>
+						Promise.resolve({
+							models: [{ name: "nomic-embed-text:latest" }],
+						}),
+				} as Response),
+			)
+
+			// Mock successful /api/embed test call with 4096-dimension embedding (like qwen3-embedding)
+			const largeEmbedding = new Array(4096).fill(0).map((_, i) => i * 0.001)
+			mockFetch.mockImplementationOnce(() =>
+				Promise.resolve({
+					ok: true,
+					status: 200,
+					json: () =>
+						Promise.resolve({
+							embeddings: [largeEmbedding],
+						}),
+				} as Response),
+			)
+
+			const result = await embedder.validateConfiguration()
+
+			expect(result.valid).toBe(true)
+			expect(result.detectedDimension).toBe(4096)
+		})
+
 		it("should fail validation when service is not available", async () => {
 			mockFetch.mockRejectedValueOnce(new Error("ECONNREFUSED"))
 
diff --git a/src/services/code-index/embedders/__tests__/openai-compatible.spec.ts b/src/services/code-index/embedders/__tests__/openai-compatible.spec.ts
index ecde7691515..3f16a67753e 100644
--- a/src/services/code-index/embedders/__tests__/openai-compatible.spec.ts
+++ b/src/services/code-index/embedders/__tests__/openai-compatible.spec.ts
@@ -978,6 +978,7 @@ describe("OpenAICompatibleEmbedder", () => {
 
 			expect(result.valid).toBe(true)
 			expect(result.error).toBeUndefined()
+			expect(result.detectedDimension).toBe(3) // Auto-detected from array embedding
 			expect(mockEmbeddingsCreate).toHaveBeenCalledWith({
 				input: ["test"],
 				model: testModelId,
@@ -1003,6 +1004,7 @@ describe("OpenAICompatibleEmbedder", () => {
 
 			expect(result.valid).toBe(true)
 			expect(result.error).toBeUndefined()
+			expect(result.detectedDimension).toBe(3) // Auto-detected from array embedding
 			expect(mockFetch).toHaveBeenCalledWith(
 				fullUrl,
 				expect.objectContaining({
@@ -1014,6 +1016,25 @@ describe("OpenAICompatibleEmbedder", () => {
 			)
 		})
 
+		it("should detect dimension from base64 encoded embedding", async () => {
+			embedder = new OpenAICompatibleEmbedder(testBaseUrl, testApiKey, testModelId)
+
+			// Create a 1536-dimension embedding as base64 (like text-embedding-3-small)
+			const embedding = new Float32Array(1536).fill(0.1)
+			const base64String = Buffer.from(embedding.buffer).toString("base64")
+
+			const mockResponse = {
+				data: [{ embedding: base64String }],
+				usage: { prompt_tokens: 2, total_tokens: 2 },
+			}
+			mockEmbeddingsCreate.mockResolvedValue(mockResponse)
+
+			const result = await embedder.validateConfiguration()
+
+			expect(result.valid).toBe(true)
+			expect(result.detectedDimension).toBe(1536) // Auto-detected from base64 (1536 * 4 bytes / 4 = 1536)
+		})
+
 		it("should fail validation with authentication error", async () => {
 			embedder = new OpenAICompatibleEmbedder(testBaseUrl, testApiKey, testModelId)
 
diff --git a/src/services/code-index/embedders/bedrock.ts b/src/services/code-index/embedders/bedrock.ts
index e99d6ee25ec..4e9b7aca213 100644
--- a/src/services/code-index/embedders/bedrock.ts
+++ b/src/services/code-index/embedders/bedrock.ts
@@ -263,10 +263,11 @@ export class BedrockEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the Bedrock embedder configuration by attempting a minimal embedding request
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the Bedrock embedder configuration by attempting a minimal embedding request.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		return withValidationErrorHandling(async () => {
 			try {
 				// Test with a minimal embedding request
@@ -280,7 +281,10 @@ export class BedrockEmbedder implements IEmbedder {
 					}
 				}
 
-				return { valid: true }
+				// Get the dimension from the embedding
+				const detectedDimension = result.embedding.length
+
+				return { valid: true, detectedDimension }
 			} catch (error: any) {
 				// Check for specific AWS errors
 				if (error.name === "UnrecognizedClientException") {
diff --git a/src/services/code-index/embedders/gemini.ts b/src/services/code-index/embedders/gemini.ts
index 7e795875c9d..99f2118e95b 100644
--- a/src/services/code-index/embedders/gemini.ts
+++ b/src/services/code-index/embedders/gemini.ts
@@ -63,10 +63,11 @@ export class GeminiEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the Gemini embedder configuration by delegating to the underlying OpenAI-compatible embedder
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the Gemini embedder configuration by delegating to the underlying OpenAI-compatible embedder.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		try {
 			// Delegate validation to the OpenAI-compatible embedder
 			// The error messages will be specific to Gemini since we're using Gemini's base URL
diff --git a/src/services/code-index/embedders/mistral.ts b/src/services/code-index/embedders/mistral.ts
index c23bcbba1d4..0d0cb429503 100644
--- a/src/services/code-index/embedders/mistral.ts
+++ b/src/services/code-index/embedders/mistral.ts
@@ -62,10 +62,11 @@ export class MistralEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the Mistral embedder configuration by delegating to the underlying OpenAI-compatible embedder
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the Mistral embedder configuration by delegating to the underlying OpenAI-compatible embedder.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		try {
 			// Delegate validation to the OpenAI-compatible embedder
 			// The error messages will be specific to Mistral since we're using Mistral's base URL
diff --git a/src/services/code-index/embedders/ollama.ts b/src/services/code-index/embedders/ollama.ts
index 9688a15ff04..668fc6b04b2 100644
--- a/src/services/code-index/embedders/ollama.ts
+++ b/src/services/code-index/embedders/ollama.ts
@@ -138,10 +138,11 @@ export class CodeIndexOllamaEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the Ollama embedder configuration by checking service availability and model existence
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the Ollama embedder configuration by checking service availability and model existence.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		return withValidationErrorHandling(
 			async () => {
 				// First check if Ollama service is running by trying to list models
@@ -228,7 +229,19 @@ export class CodeIndexOllamaEmbedder implements IEmbedder {
 					}
 				}
 
-				return { valid: true }
+				// Parse the test response to get the embedding dimension
+				const testData = await testResponse.json()
+				const embeddings = testData.embeddings
+				let detectedDimension: number | undefined
+
+				if (embeddings && Array.isArray(embeddings) && embeddings.length > 0) {
+					const firstEmbedding = embeddings[0]
+					if (Array.isArray(firstEmbedding)) {
+						detectedDimension = firstEmbedding.length
+					}
+				}
+
+				return { valid: true, detectedDimension }
 			},
 			"ollama",
 			{
diff --git a/src/services/code-index/embedders/openai-compatible.ts b/src/services/code-index/embedders/openai-compatible.ts
index 6eaf2b6c2c1..9252797d173 100644
--- a/src/services/code-index/embedders/openai-compatible.ts
+++ b/src/services/code-index/embedders/openai-compatible.ts
@@ -357,10 +357,11 @@ export class OpenAICompatibleEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the OpenAI-compatible embedder configuration by testing endpoint connectivity and API key
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the OpenAI-compatible embedder configuration by testing endpoint connectivity and API key.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		return withValidationErrorHandling(async () => {
 			try {
 				// Test with a minimal embedding request
@@ -389,7 +390,20 @@ export class OpenAICompatibleEmbedder implements IEmbedder {
 					}
 				}
 
-				return { valid: true }
+				// Convert base64 embedding to get the actual dimension
+				let detectedDimension: number | undefined
+				const firstItem = response.data[0]
+				if (firstItem?.embedding) {
+					if (typeof firstItem.embedding === "string") {
+						// Decode base64 to get float32 array length
+						const buffer = Buffer.from(firstItem.embedding, "base64")
+						detectedDimension = buffer.byteLength / 4 // 4 bytes per float32
+					} else if (Array.isArray(firstItem.embedding)) {
+						detectedDimension = firstItem.embedding.length
+					}
+				}
+
+				return { valid: true, detectedDimension }
 			} catch (error) {
 				// Capture telemetry for validation errors
 				TelemetryService.instance.captureEvent(TelemetryEventName.CODE_INDEX_ERROR, {
diff --git a/src/services/code-index/embedders/openai.ts b/src/services/code-index/embedders/openai.ts
index b993e280d98..e67af683384 100644
--- a/src/services/code-index/embedders/openai.ts
+++ b/src/services/code-index/embedders/openai.ts
@@ -187,10 +187,11 @@ export class OpenAiEmbedder extends OpenAiNativeHandler implements IEmbedder {
 	}
 
 	/**
-	 * Validates the OpenAI embedder configuration by attempting a minimal embedding request
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the OpenAI embedder configuration by attempting a minimal embedding request.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		return withValidationErrorHandling(async () => {
 			try {
 				// Test with a minimal embedding request
@@ -207,7 +208,10 @@ export class OpenAiEmbedder extends OpenAiNativeHandler implements IEmbedder {
 					}
 				}
 
-				return { valid: true }
+				// Get the dimension from the first embedding
+				const detectedDimension = response.data[0]?.embedding?.length
+
+				return { valid: true, detectedDimension }
 			} catch (error) {
 				// Capture telemetry for validation errors
 				TelemetryService.instance.captureEvent(TelemetryEventName.CODE_INDEX_ERROR, {
diff --git a/src/services/code-index/embedders/openrouter.ts b/src/services/code-index/embedders/openrouter.ts
index 2ffdd7afb64..79785d22d20 100644
--- a/src/services/code-index/embedders/openrouter.ts
+++ b/src/services/code-index/embedders/openrouter.ts
@@ -286,10 +286,11 @@ export class OpenRouterEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the OpenRouter embedder configuration by testing API connectivity
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the OpenRouter embedder configuration by testing API connectivity.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		return withValidationErrorHandling(async () => {
 			try {
 				// Test with a minimal embedding request
@@ -324,7 +325,20 @@ export class OpenRouterEmbedder implements IEmbedder {
 					}
 				}
 
-				return { valid: true }
+				// Detect the embedding dimension from the response
+				let detectedDimension: number | undefined
+				const firstItem = response.data[0]
+				if (firstItem?.embedding) {
+					if (typeof firstItem.embedding === "string") {
+						// Decode base64 to get float32 array length
+						const buffer = Buffer.from(firstItem.embedding, "base64")
+						detectedDimension = buffer.byteLength / 4 // 4 bytes per float32
+					} else if (Array.isArray(firstItem.embedding)) {
+						detectedDimension = firstItem.embedding.length
+					}
+				}
+
+				return { valid: true, detectedDimension }
 			} catch (error) {
 				// Capture telemetry for validation errors
 				TelemetryService.instance.captureEvent(TelemetryEventName.CODE_INDEX_ERROR, {
diff --git a/src/services/code-index/embedders/vercel-ai-gateway.ts b/src/services/code-index/embedders/vercel-ai-gateway.ts
index ec0888cd8b5..86c5817b29a 100644
--- a/src/services/code-index/embedders/vercel-ai-gateway.ts
+++ b/src/services/code-index/embedders/vercel-ai-gateway.ts
@@ -71,10 +71,11 @@ export class VercelAiGatewayEmbedder implements IEmbedder {
 	}
 
 	/**
-	 * Validates the Vercel AI Gateway embedder configuration by delegating to the underlying OpenAI-compatible embedder
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Validates the Vercel AI Gateway embedder configuration by delegating to the underlying OpenAI-compatible embedder.
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	async validateConfiguration(): Promise<{ valid: boolean; error?: string }> {
+	async validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		try {
 			// Delegate validation to the OpenAI-compatible embedder
 			// The error messages will be specific to Vercel AI Gateway since we're using Vercel's base URL
diff --git a/src/services/code-index/interfaces/embedder.ts b/src/services/code-index/interfaces/embedder.ts
index aa8515d6986..0d36b568ecd 100644
--- a/src/services/code-index/interfaces/embedder.ts
+++ b/src/services/code-index/interfaces/embedder.ts
@@ -13,9 +13,10 @@ export interface IEmbedder {
 
 	/**
 	 * Validates the embedder configuration by testing connectivity and credentials.
-	 * @returns Promise resolving to validation result with success status and optional error message
+	 * Also detects the actual embedding dimension from a test embedding.
+	 * @returns Promise resolving to validation result with success status, optional error message, and detected dimension
 	 */
-	validateConfiguration(): Promise<{ valid: boolean; error?: string }>
+	validateConfiguration(): Promise<{ valid: boolean; error?: string; detectedDimension?: number }>
 
 	get embedderInfo(): EmbedderInfo
 }
diff --git a/src/services/code-index/manager.ts b/src/services/code-index/manager.ts
index dd79a3f1616..7f9745832b9 100644
--- a/src/services/code-index/manager.ts
+++ b/src/services/code-index/manager.ts
@@ -332,15 +332,10 @@ export class CodeIndexManager {
 		const rooIgnoreController = new RooIgnoreController(workspacePath)
 		await rooIgnoreController.initialize()
 
-		// (Re)Create shared service instances
-		const { embedder, vectorStore, scanner, fileWatcher } = this._serviceFactory.createServices(
-			this.context,
-			this._cacheManager!,
-			ignoreInstance,
-			rooIgnoreController,
-		)
+		// Create embedder first to validate and detect embedding dimension
+		const embedder = this._serviceFactory.createEmbedder()
 
-		// Validate embedder configuration before proceeding
+		// Validate embedder configuration and detect actual embedding dimension
 		const validationResult = await this._serviceFactory.validateEmbedder(embedder)
 		if (!validationResult.valid) {
 			const errorMessage = validationResult.error || "Embedder configuration validation failed"
@@ -348,6 +343,20 @@ export class CodeIndexManager {
 			throw new Error(errorMessage)
 		}
 
+		// Use the auto-detected dimension if available
+		// This ensures we always use the actual dimension from the model,
+		// preventing mismatches between configured and actual dimensions (Issue #10991)
+		const detectedDimension = validationResult.detectedDimension
+
+		// (Re)Create shared service instances with the detected dimension
+		const { vectorStore, scanner, fileWatcher } = this._serviceFactory.createServices(
+			this.context,
+			this._cacheManager!,
+			ignoreInstance,
+			rooIgnoreController,
+			detectedDimension,
+		)
+
 		// (Re)Initialize orchestrator
 		this._orchestrator = new CodeIndexOrchestrator(
 			this._configManager!,
diff --git a/src/services/code-index/service-factory.ts b/src/services/code-index/service-factory.ts
index d23eff4810b..b28293b1ae9 100644
--- a/src/services/code-index/service-factory.ts
+++ b/src/services/code-index/service-factory.ts
@@ -112,10 +112,13 @@ export class CodeIndexServiceFactory {
 
 	/**
 	 * Validates an embedder instance to ensure it's properly configured.
+	 * Also captures the detected embedding dimension from the test embedding.
 	 * @param embedder The embedder instance to validate
-	 * @returns Promise resolving to validation result
+	 * @returns Promise resolving to validation result with optional detected dimension
 	 */
-	public async validateEmbedder(embedder: IEmbedder): Promise<{ valid: boolean; error?: string }> {
+	public async validateEmbedder(
+		embedder: IEmbedder,
+	): Promise<{ valid: boolean; error?: string; detectedDimension?: number }> {
 		try {
 			return await embedder.validateConfiguration()
 		} catch (error) {
@@ -136,8 +139,10 @@ export class CodeIndexServiceFactory {
 
 	/**
 	 * Creates a vector store instance using the current configuration.
+	 * @param detectedDimension Optional embedding dimension auto-detected from a test embedding.
+	 *                          When provided, this takes priority over profile-based or manual dimensions.
 	 */
-	public createVectorStore(): IVectorStore {
+	public createVectorStore(detectedDimension?: number): IVectorStore {
 		const config = this.configManager.getConfig()
 
 		const provider = config.embedderProvider as EmbedderProvider
@@ -147,12 +152,20 @@ export class CodeIndexServiceFactory {
 
 		let vectorSize: number | undefined
 
-		// First try to get the model-specific dimension from profiles
-		vectorSize = getModelDimension(provider, modelId)
+		// Priority order for vector dimension:
+		// 1. Auto-detected dimension from test embedding (most reliable)
+		// 2. Model-specific dimension from profiles
+		// 3. Manual dimension from config (fallback for unknown models)
+		if (detectedDimension && detectedDimension > 0) {
+			vectorSize = detectedDimension
+		} else {
+			// Try to get the model-specific dimension from profiles
+			vectorSize = getModelDimension(provider, modelId)
 
-		// Only use manual dimension if model doesn't have a built-in dimension
-		if (!vectorSize && config.modelDimension && config.modelDimension > 0) {
-			vectorSize = config.modelDimension
+			// Only use manual dimension if model doesn't have a built-in dimension
+			if (!vectorSize && config.modelDimension && config.modelDimension > 0) {
+				vectorSize = config.modelDimension
+			}
 		}
 
 		if (vectorSize === undefined || vectorSize <= 0) {
@@ -230,6 +243,11 @@ export class CodeIndexServiceFactory {
 
 	/**
 	 * Creates all required service dependencies if the service is properly configured.
+	 * @param context VSCode extension context
+	 * @param cacheManager Cache manager instance
+	 * @param ignoreInstance Ignore instance for .gitignore
+	 * @param rooIgnoreController Optional RooIgnore controller
+	 * @param detectedDimension Optional auto-detected embedding dimension from validation
 	 * @throws Error if the service is not properly configured
 	 */
 	public createServices(
@@ -237,6 +255,7 @@ export class CodeIndexServiceFactory {
 		cacheManager: CacheManager,
 		ignoreInstance: Ignore,
 		rooIgnoreController?: RooIgnoreController,
+		detectedDimension?: number,
 	): {
 		embedder: IEmbedder
 		vectorStore: IVectorStore
@@ -249,7 +268,7 @@ export class CodeIndexServiceFactory {
 		}
 
 		const embedder = this.createEmbedder()
-		const vectorStore = this.createVectorStore()
+		const vectorStore = this.createVectorStore(detectedDimension)
 		const parser = codeParser
 		const scanner = this.createDirectoryScanner(embedder, vectorStore, parser, ignoreInstance)
 		const fileWatcher = this.createFileWatcher(