diff --git a/src/Azure.DataApiBuilder.Mcp/Core/McpStdioServer.cs b/src/Azure.DataApiBuilder.Mcp/Core/McpStdioServer.cs
index aef3b63dcc..49974296be 100644
--- a/src/Azure.DataApiBuilder.Mcp/Core/McpStdioServer.cs
+++ b/src/Azure.DataApiBuilder.Mcp/Core/McpStdioServer.cs
@@ -6,6 +6,7 @@
 using Azure.DataApiBuilder.Config.ObjectModel;
 using Azure.DataApiBuilder.Core.AuthenticationHelpers.AuthenticationSimulator;
 using Azure.DataApiBuilder.Core.Configurations;
+using Azure.DataApiBuilder.Core.Services.MetadataProviders;
 using Azure.DataApiBuilder.Core.Telemetry;
 using Azure.DataApiBuilder.Mcp.Model;
 using Azure.DataApiBuilder.Mcp.Telemetry;
@@ -30,6 +31,8 @@ public class McpStdioServer : IMcpStdioServer
         private readonly McpStdoutWriter _stdoutWriter;
         private readonly TextReader? _inputReader;
         private readonly string _protocolVersion;
+        private readonly object _initializationLock = new();
+        private Task? _initializationTask;
 
         private const int MAX_LINE_LENGTH = 1024 * 1024; // 1 MB limit for incoming JSON-RPC requests
 
@@ -134,7 +137,7 @@ public async Task RunAsync(CancellationToken cancellationToken)
                                 break;
 
                             case "tools/list":
-                                HandleListTools(id);
+                                await HandleListToolsAsync(id);
                                 break;
 
                             case "tools/call":
@@ -284,8 +287,10 @@ private void HandleInitialize(JsonElement? id, JsonElement root)
         /// <param name="id">
         /// The request identifier extracted from the incoming JSON-RPC request. Used to correlate the response with the request.
         /// </param>
-        private void HandleListTools(JsonElement? id)
+        private async Task HandleListToolsAsync(JsonElement? id)
         {
+            await EnsureToolsInitializedAsync();
+
             List<object> toolsWire = new();
             int count = 0;
 
@@ -308,6 +313,24 @@ private void HandleListTools(JsonElement? id)
             WriteResult(id, new { tools = toolsWire });
         }
 
+        private Task EnsureToolsInitializedAsync()
+        {
+            lock (_initializationLock)
+            {
+                return _initializationTask ??= InitializeToolsAsync();
+            }
+        }
+
+        private async Task InitializeToolsAsync()
+        {
+            IMetadataProviderFactory metadataProviderFactory =
+                _serviceProvider.GetRequiredService<IMetadataProviderFactory>();
+            await metadataProviderFactory.InitializeAsync();
+
+            IEnumerable<IMcpTool> tools = _serviceProvider.GetServices<IMcpTool>();
+            McpToolRegistry.InitializeAndRegisterTools(tools, _toolRegistry, _serviceProvider);
+        }
+
         /// <summary>
         /// Handles the "logging/setLevel" JSON-RPC method by updating the runtime log level.
         /// </summary>
@@ -455,6 +478,8 @@ private async Task HandleCallToolAsync(JsonElement? id, JsonElement root, Cancel
                 return;
             }
 
+            await EnsureToolsInitializedAsync();
+
             if (!_toolRegistry.TryGetTool(toolName!, out IMcpTool? tool) || tool is null)
             {
                 WriteError(id, McpStdioJsonRpcErrorCodes.INVALID_PARAMS, $"Tool not found: {toolName}");
diff --git a/src/Service.Tests/UnitTests/McpStdioServerRunAsyncTests.cs b/src/Service.Tests/UnitTests/McpStdioServerRunAsyncTests.cs
index 224d534158..fd5c955a25 100644
--- a/src/Service.Tests/UnitTests/McpStdioServerRunAsyncTests.cs
+++ b/src/Service.Tests/UnitTests/McpStdioServerRunAsyncTests.cs
@@ -4,10 +4,18 @@
 #nullable enable
 
 using System;
+using System.Collections.Generic;
+using System.Diagnostics.CodeAnalysis;
 using System.IO;
 using System.Text.Json;
 using System.Threading;
 using System.Threading.Tasks;
+using Azure.DataApiBuilder.Config;
+using Azure.DataApiBuilder.Config.DatabasePrimitives;
+using Azure.DataApiBuilder.Config.ObjectModel;
+using Azure.DataApiBuilder.Core.Configurations;
+using Azure.DataApiBuilder.Core.Services;
+using Azure.DataApiBuilder.Core.Services.MetadataProviders;
 using Azure.DataApiBuilder.Mcp.Core;
 using Azure.DataApiBuilder.Mcp.Model;
 using Microsoft.Extensions.DependencyInjection;
@@ -91,6 +99,63 @@ public async Task RunAsync_OutOfRangeNumericId_PreservesIdAndContinuesProcessing
             Assert.IsTrue(shutdownResponse.RootElement.GetProperty("result").GetProperty("ok").GetBoolean());
         }
 
+        [TestMethod]
+        public async Task RunAsync_InitializeRespondsBeforeMetadataInferenceCompletes()
+        {
+            const string INPUT =
+                "{\"jsonrpc\":\"2.0\",\"id\":1,\"method\":\"initialize\",\"params\":{}}\n" +
+                "{\"jsonrpc\":\"2.0\",\"method\":\"notifications/initialized\",\"params\":{}}\n" +
+                "{\"jsonrpc\":\"2.0\",\"id\":2,\"method\":\"tools/list\",\"params\":{}}\n" +
+                "{\"jsonrpc\":\"2.0\",\"id\":3,\"method\":\"tools/list\",\"params\":{}}\n" +
+                "{\"jsonrpc\":\"2.0\",\"id\":4,\"method\":\"shutdown\"}\n";
+
+            SignalingTextWriter stdoutCapture = new();
+            BlockingMetadataProviderFactory metadataProviderFactory = new();
+            RuntimeConfig runtimeConfig = new(
+                Schema: RuntimeConfig.DEFAULT_CONFIG_SCHEMA_LINK,
+                DataSource: null,
+                Entities: new RuntimeEntities(new Dictionary<string, Entity>()),
+                Runtime: new RuntimeOptions(
+                    Rest: null,
+                    GraphQL: null,
+                    Mcp: new McpRuntimeOptions(),
+                    Host: null));
+            RuntimeConfigProvider runtimeConfigProvider = new StubRuntimeConfigProvider(runtimeConfig);
+
+            ServiceProvider serviceProvider = new ServiceCollection()
+                .AddSingleton(new McpStdoutWriter(stdoutCapture))
+                .AddSingleton<McpToolRegistry>()
+                .AddSingleton<IMetadataProviderFactory>(metadataProviderFactory)
+                .AddSingleton(runtimeConfigProvider)
+                .BuildServiceProvider();
+            McpStdioServer server = new(
+                serviceProvider.GetRequiredService<McpToolRegistry>(),
+                serviceProvider,
+                new StringReader(INPUT));
+
+            Task runTask = server.RunAsync(CancellationToken.None);
+
+            string initializeResponse = await stdoutCapture.FirstLineWritten.Task.WaitAsync(TimeSpan.FromSeconds(5));
+            await metadataProviderFactory.InitializeStarted.Task.WaitAsync(TimeSpan.FromSeconds(5));
+
+            using (JsonDocument response = JsonDocument.Parse(initializeResponse))
+            {
+                Assert.AreEqual(1, response.RootElement.GetProperty("id").GetInt32(),
+                    "Initialize must respond before metadata inference completes.");
+            }
+
+            Assert.AreEqual(1, stdoutCapture.LineCount,
+                "tools/list must wait until metadata inference and tool registration complete.");
+
+            metadataProviderFactory.CompleteInitialization();
+            await runTask.WaitAsync(TimeSpan.FromSeconds(5));
+
+            Assert.AreEqual(4, stdoutCapture.LineCount,
+                "Expected initialize, two tools/list, and shutdown responses.");
+            Assert.AreEqual(1, metadataProviderFactory.InitializeAsyncCallCount,
+                "Metadata inference must run exactly once.");
+        }
+
         private static (McpStdioServer server, StringWriter stdoutCapture) CreateServerWithCapturedOutput(TextReader inputReader)
         {
             StringWriter stdoutCapture = new();
@@ -108,5 +173,87 @@ private static (McpStdioServer server, StringWriter stdoutCapture) CreateServerW
 
             return (server, stdoutCapture);
         }
+
+        private sealed class SignalingTextWriter : StringWriter
+        {
+            public TaskCompletionSource<string> FirstLineWritten { get; } =
+                new(TaskCreationOptions.RunContinuationsAsynchronously);
+
+            public int LineCount { get; private set; }
+
+            public override void WriteLine(string? value)
+            {
+                base.WriteLine(value);
+                LineCount++;
+                FirstLineWritten.TrySetResult(value ?? string.Empty);
+            }
+        }
+
+        private sealed class BlockingMetadataProviderFactory : IMetadataProviderFactory
+        {
+            private readonly TaskCompletionSource _completeInitialization =
+                new(TaskCreationOptions.RunContinuationsAsynchronously);
+
+            public TaskCompletionSource InitializeStarted { get; } = new(TaskCreationOptions.RunContinuationsAsynchronously);
+
+            public int InitializeAsyncCallCount { get; private set; }
+
+            public async Task InitializeAsync()
+            {
+                InitializeAsyncCallCount++;
+                InitializeStarted.TrySetResult();
+                await _completeInitialization.Task;
+            }
+
+            public void CompleteInitialization()
+            {
+                _completeInitialization.TrySetResult();
+            }
+
+            public ISqlMetadataProvider GetMetadataProvider(string dataSourceName)
+                => throw new NotImplementedException();
+
+            public IEnumerable<ISqlMetadataProvider> ListMetadataProviders()
+                => Array.Empty<ISqlMetadataProvider>();
+
+            public List<Exception> GetAllMetadataExceptions()
+                => new();
+
+            public void InitializeAsync(
+                Dictionary<string, Dictionary<string, DatabaseObject>> entityToDatabaseObjectMap,
+                Dictionary<string, Dictionary<string, string>> graphQLStoredProcedureExposedNameToEntityNameMap)
+            {
+                InitializeAsyncCallCount++;
+            }
+        }
+
+        private sealed class StubRuntimeConfigProvider : RuntimeConfigProvider
+        {
+            private readonly RuntimeConfig _runtimeConfig;
+
+            public StubRuntimeConfigProvider(RuntimeConfig runtimeConfig) : base(new StubRuntimeConfigLoader())
+            {
+                _runtimeConfig = runtimeConfig;
+            }
+
+            public override RuntimeConfig GetConfig()
+            {
+                return _runtimeConfig;
+            }
+        }
+
+        private sealed class StubRuntimeConfigLoader : RuntimeConfigLoader
+        {
+            public override bool TryLoadKnownConfig([NotNullWhen(true)] out RuntimeConfig? config, bool replaceEnvVar = false)
+            {
+                config = null;
+                return false;
+            }
+
+            public override string GetPublishedDraftSchemaLink()
+            {
+                return RuntimeConfig.DEFAULT_CONFIG_SCHEMA_LINK;
+            }
+        }
     }
 }
diff --git a/src/Service/Utilities/McpStdioHelper.cs b/src/Service/Utilities/McpStdioHelper.cs
index 4ee403b98e..169fa87982 100644
--- a/src/Service/Utilities/McpStdioHelper.cs
+++ b/src/Service/Utilities/McpStdioHelper.cs
@@ -78,13 +78,6 @@ public static bool RunMcpStdioHost(IHost host)
         {
             try
             {
-                Mcp.Core.McpToolRegistry registry =
-                    host.Services.GetRequiredService<Mcp.Core.McpToolRegistry>();
-                IEnumerable<Mcp.Model.IMcpTool> tools =
-                    host.Services.GetServices<Mcp.Model.IMcpTool>();
-
-                Mcp.Core.McpToolRegistry.InitializeAndRegisterTools(tools, registry, host.Services);
-
                 IHostApplicationLifetime lifetime =
                     host.Services.GetRequiredService<IHostApplicationLifetime>();
                 Mcp.Core.IMcpStdioServer stdio =