diff --git a/README.MD b/README.MD
index 61b3335..1997a96 100644
--- a/README.MD
+++ b/README.MD
@@ -80,7 +80,7 @@ var response = await chatClient.GetResponseAsync(
 
 Here is an example of how to create an MCP server and register all tools from the current application.
 It includes a simple echo tool as an example (this is included in the same file here for easy of copy and paste, but it needn't be in the same file...
-the employed overload of `WithTools` examines the current assembly for classes with the `McpToolType` attribute, and registers all methods with the
+the employed overload of `WithTools` examines the current assembly for classes with the `McpServerToolType` attribute, and registers all methods with the
 `McpTool` attribute as tools.)
 
 ```csharp
diff --git a/src/ModelContextProtocol/README.md b/src/ModelContextProtocol/README.md
index a109add..90a3990 100644
--- a/src/ModelContextProtocol/README.md
+++ b/src/ModelContextProtocol/README.md
@@ -85,7 +85,7 @@ var response = await chatClient.GetResponseAsync(
 
 Here is an example of how to create an MCP server and register all tools from the current application.
 It includes a simple echo tool as an example (this is included in the same file here for easy of copy and paste, but it needn't be in the same file...
-the employed overload of `WithTools` examines the current assembly for classes with the `McpToolType` attribute, and registers all methods with the
+the employed overload of `WithTools` examines the current assembly for classes with the `McpServerToolType` attribute, and registers all methods with the
 `McpTool` attribute as tools.)
 
 ```csharp
@@ -101,7 +101,7 @@ builder.Services
     .WithTools();
 await builder.Build().RunAsync();
 
-[McpToolType]
+[McpServerToolType]
 public static class EchoTool
 {
     [McpTool, Description("Echoes the message back to the client.")]
diff --git a/src/ModelContextProtocol/Server/McpServer.cs b/src/ModelContextProtocol/Server/McpServer.cs
index 4c0c6b5..7f425b1 100644
--- a/src/ModelContextProtocol/Server/McpServer.cs
+++ b/src/ModelContextProtocol/Server/McpServer.cs
@@ -15,6 +15,8 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
 {
     private readonly IServerTransport? _serverTransport;
     private readonly string _serverDescription;
+    private readonly EventHandler? _toolsChangedDelegate;
+
     private volatile bool _isInitializing;
 
     /// <summary>
@@ -32,17 +34,29 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
         Throw.IfNull(options);
 
         _serverTransport = transport as IServerTransport;
-        ServerInstructions = options.ServerInstructions;
+        ServerOptions = options;
         Services = serviceProvider;
         _serverDescription = $"{options.ServerInfo.Name} {options.ServerInfo.Version}";
+        _toolsChangedDelegate = delegate
+        {
+            _ = SendMessageAsync(new JsonRpcNotification()
+            {
+                Method = NotificationMethods.ToolListChangedNotification,
+            });
+        };
 
         AddNotificationHandler("notifications/initialized", _ =>
         {
+            if (ServerOptions.Capabilities?.Tools?.ToolCollection is { } tools)
+            {
+                tools.Changed += _toolsChangedDelegate;
+            }
+
             IsInitialized = true;
             return Task.CompletedTask;
         });
 
-        SetToolsHandler(ref options);
+        SetToolsHandler(options);
 
         SetInitializeHandler(options);
         SetCompletionHandler(options);
@@ -50,18 +64,15 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
         SetPromptsHandler(options);
         SetResourcesHandler(options);
         SetSetLoggingLevelHandler(options);
-
-        ServerOptions = options;
     }
 
+    public ServerCapabilities? ServerCapabilities { get; set; }
+
     public ClientCapabilities? ClientCapabilities { get; set; }
 
     /// <inheritdoc />
     public Implementation? ClientInfo { get; set; }
 
-    /// <inheritdoc />
-    public string? ServerInstructions { get; set; }
-
     /// <inheritdoc />
     public McpServerOptions ServerOptions { get; }
 
@@ -111,6 +122,15 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
         }
     }
 
+    protected override Task CleanupAsync()
+    {
+        if (ServerOptions.Capabilities?.Tools?.ToolCollection is { } tools)
+        {
+            tools.Changed -= _toolsChangedDelegate;
+        }
+        return base.CleanupAsync();
+    }
+
     private void SetPingHandler()
     {
         SetRequestHandler<JsonNode, PingResult>("ping",
@@ -127,9 +147,9 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
                 return Task.FromResult(new InitializeResult()
                 {
                     ProtocolVersion = options.ProtocolVersion,
-                    Instructions = ServerInstructions,
+                    Instructions = options.ServerInstructions,
                     ServerInfo = options.ServerInfo,
-                    Capabilities = options.Capabilities ?? new ServerCapabilities(),
+                    Capabilities = ServerCapabilities ?? new(),
                 });
             });
     }
@@ -198,7 +218,7 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
         SetRequestHandler<GetPromptRequestParams, GetPromptResult>("prompts/get", (request, ct) => getPromptHandler(new(this, request), ct));
     }
 
-    private void SetToolsHandler(ref McpServerOptions options)
+    private void SetToolsHandler(McpServerOptions options)
     {
         ToolsCapability? toolsCapability = options.Capabilities?.Tools;
         var listToolsHandler = toolsCapability?.ListToolsHandler;
@@ -261,25 +281,25 @@ internal sealed class McpServer : McpJsonRpcEndpoint, IMcpServer
                 return tool.InvokeAsync(request, cancellationToken);
             };
 
-            toolsCapability ??= new();
-            toolsCapability.CallToolHandler = callToolHandler;
-            toolsCapability.ListToolsHandler = listToolsHandler;
-            toolsCapability.ToolCollection = tools;
-            toolsCapability.ListChanged = true;
-
-            options.Capabilities ??= new();
-            options.Capabilities.Tools = toolsCapability;
-
-            tools.Changed += delegate
+            ServerCapabilities = new()
             {
-                _ = SendMessageAsync(new JsonRpcNotification()
+                Experimental = options.Capabilities?.Experimental,
+                Logging = options.Capabilities?.Logging,
+                Prompts = options.Capabilities?.Prompts,
+                Resources = options.Capabilities?.Resources,
+                Tools = new()
                 {
-                    Method = NotificationMethods.ToolListChangedNotification,
-                });
+                    ListToolsHandler = listToolsHandler,
+                    CallToolHandler = callToolHandler,
+                    ToolCollection = tools,
+                    ListChanged = true,
+                }
             };
         }
         else
         {
+            ServerCapabilities = options.Capabilities;
+
             if (toolsCapability is null)
             {
                 // No tools, and no tools capability was declared, so nothing to do.
diff --git a/src/ModelContextProtocol/Shared/McpJsonRpcEndpoint.cs b/src/ModelContextProtocol/Shared/McpJsonRpcEndpoint.cs
index 175a60b..90824c5 100644
--- a/src/ModelContextProtocol/Shared/McpJsonRpcEndpoint.cs
+++ b/src/ModelContextProtocol/Shared/McpJsonRpcEndpoint.cs
@@ -359,7 +359,7 @@ internal abstract class McpJsonRpcEndpoint : IAsyncDisposable
     /// Cleans up the endpoint and releases resources.
     /// </summary>
     /// <returns></returns>
-    protected async Task CleanupAsync()
+    protected virtual async Task CleanupAsync()
     {
         if (_isDisposed)
             return;
diff --git a/tests/ModelContextProtocol.Tests/Client/McpClientExtensionsTests.cs b/tests/ModelContextProtocol.Tests/Client/McpClientExtensionsTests.cs
index 43d5131..03d0e99 100644
--- a/tests/ModelContextProtocol.Tests/Client/McpClientExtensionsTests.cs
+++ b/tests/ModelContextProtocol.Tests/Client/McpClientExtensionsTests.cs
@@ -38,8 +38,8 @@ public class McpClientExtensionsTests
     {
         await _server.StartAsync(TestContext.Current.CancellationToken);
 
-        var stdin = new StreamReader(_serverToClientPipe.Reader.AsStream());
-        var stdout = new StreamWriter(_clientToServerPipe.Writer.AsStream());
+        var serverStdinWriter = new StreamWriter(_clientToServerPipe.Writer.AsStream());
+        var serverStdoutReader = new StreamReader(_serverToClientPipe.Reader.AsStream());
 
         var serverConfig = new McpServerConfig()
         {
@@ -50,7 +50,7 @@ public class McpClientExtensionsTests
 
         return await McpClientFactory.CreateAsync(
             serverConfig,
-            createTransportFunc: (_, _) => new StreamClientTransport(stdin, stdout),
+            createTransportFunc: (_, _) => new StreamClientTransport(serverStdinWriter, serverStdoutReader),
             cancellationToken: TestContext.Current.CancellationToken);
     }
 
diff --git a/tests/ModelContextProtocol.Tests/Configuration/McpServerBuilderExtensionsToolsTests.cs b/tests/ModelContextProtocol.Tests/Configuration/McpServerBuilderExtensionsToolsTests.cs
index dbf1353..3ae3130 100644
--- a/tests/ModelContextProtocol.Tests/Configuration/McpServerBuilderExtensionsToolsTests.cs
+++ b/tests/ModelContextProtocol.Tests/Configuration/McpServerBuilderExtensionsToolsTests.cs
@@ -11,38 +11,45 @@ using System.Text.RegularExpressions;
 using Microsoft.Extensions.AI;
 using System.Threading.Channels;
 using ModelContextProtocol.Protocol.Messages;
+using Microsoft.Extensions.Options;
+using ModelContextProtocol.Tests.Utils;
+using Microsoft.Extensions.Logging;
 
 namespace ModelContextProtocol.Tests.Configuration;
 
-public class McpServerBuilderExtensionsToolsTests : IAsyncDisposable
+public class McpServerBuilderExtensionsToolsTests : LoggedTest, IAsyncDisposable
 {
-    private Pipe _clientToServerPipe = new();
-    private Pipe _serverToClientPipe = new();
+    private readonly Pipe _clientToServerPipe = new();
+    private readonly Pipe _serverToClientPipe = new();
+    private readonly ServiceProvider _serviceProvider;
     private readonly IMcpServerBuilder _builder;
     private readonly IMcpServer _server;
 
-    public McpServerBuilderExtensionsToolsTests()
+    public McpServerBuilderExtensionsToolsTests(ITestOutputHelper testOutputHelper)
+        : base(testOutputHelper)
     {
         ServiceCollection sc = new();
+        sc.AddSingleton(LoggerFactory);
         sc.AddSingleton<IServerTransport>(new StdioServerTransport("TestServer", _clientToServerPipe.Reader.AsStream(), _serverToClientPipe.Writer.AsStream()));
         sc.AddSingleton(new ObjectWithId());
         _builder = sc.AddMcpServer().WithTools<EchoTool>();
-        _server = sc.BuildServiceProvider().GetRequiredService<IMcpServer>();
+        _serviceProvider = sc.BuildServiceProvider();
+        _server = _serviceProvider.GetRequiredService<IMcpServer>();
     }
 
     public ValueTask DisposeAsync()
     {
         _clientToServerPipe.Writer.Complete();
         _serverToClientPipe.Writer.Complete();
-        return _server.DisposeAsync();
+        return _serviceProvider.DisposeAsync();
     }
 
     private async Task<IMcpClient> CreateMcpClientForServer()
     {
         await _server.StartAsync(TestContext.Current.CancellationToken);
 
-        var stdin = new StreamReader(_serverToClientPipe.Reader.AsStream());
-        var stdout = new StreamWriter(_clientToServerPipe.Writer.AsStream());
+        var serverStdinWriter = new StreamWriter(_clientToServerPipe.Writer.AsStream());
+        var serverStdoutReader = new StreamReader(_serverToClientPipe.Reader.AsStream());
 
         var serverConfig = new McpServerConfig()
         {
@@ -53,7 +60,7 @@ public class McpServerBuilderExtensionsToolsTests : IAsyncDisposable
 
         return await McpClientFactory.CreateAsync(
             serverConfig,
-            createTransportFunc: (_, _) => new StreamClientTransport(stdin, stdout),
+            createTransportFunc: (_, _) => new StreamClientTransport(serverStdinWriter, serverStdoutReader),
             cancellationToken: TestContext.Current.CancellationToken);
     }
 
@@ -86,6 +93,63 @@ public class McpServerBuilderExtensionsToolsTests : IAsyncDisposable
         Assert.Equal("Echoes the input back to the client.", doubleEchoTool.Description);
     }
 
+
+    [Fact]
+    public async Task Can_Create_Multiple_Servers_From_Options_And_List_Registered_Tools()
+    {
+        var options = _serviceProvider.GetRequiredService<IOptions<McpServerOptions>>().Value;
+        var loggerFactory = _serviceProvider.GetRequiredService<ILoggerFactory>();
+
+        for (int i = 0; i < 2; i++)
+        {
+            var stdinPipe = new Pipe();
+            var stdoutPipe = new Pipe();
+
+            try
+            {
+                var transport = new StdioServerTransport($"TestServer_{i}", stdinPipe.Reader.AsStream(), stdoutPipe.Writer.AsStream());
+                var server = McpServerFactory.Create(transport, options, loggerFactory, _serviceProvider);
+
+                await server.StartAsync(TestContext.Current.CancellationToken);
+
+                var serverStdinWriter = new StreamWriter(stdinPipe.Writer.AsStream());
+                var serverStdoutReader = new StreamReader(stdoutPipe.Reader.AsStream());
+
+                var serverConfig = new McpServerConfig()
+                {
+                    Id = $"TestServer_{i}",
+                    Name = $"TestServer_{i}",
+                    TransportType = "ignored",
+                };
+
+                var client = await McpClientFactory.CreateAsync(
+                    serverConfig,
+                    createTransportFunc: (_, _) => new StreamClientTransport(serverStdinWriter, serverStdoutReader),
+                    cancellationToken: TestContext.Current.CancellationToken);
+
+                var tools = await client.ListToolsAsync(TestContext.Current.CancellationToken);
+                Assert.Equal(11, tools.Count);
+
+                McpClientTool echoTool = tools.First(t => t.Name == "Echo");
+                Assert.Equal("Echo", echoTool.Name);
+                Assert.Equal("Echoes the input back to the client.", echoTool.Description);
+                Assert.Equal("object", echoTool.JsonSchema.GetProperty("type").GetString());
+                Assert.Equal(JsonValueKind.Object, echoTool.JsonSchema.GetProperty("properties").GetProperty("message").ValueKind);
+                Assert.Equal("the echoes message", echoTool.JsonSchema.GetProperty("properties").GetProperty("message").GetProperty("description").GetString());
+                Assert.Equal(1, echoTool.JsonSchema.GetProperty("required").GetArrayLength());
+
+                McpClientTool doubleEchoTool = tools.First(t => t.Name == "double_echo");
+                Assert.Equal("double_echo", doubleEchoTool.Name);
+                Assert.Equal("Echoes the input back to the client.", doubleEchoTool.Description);
+            }
+            finally
+            {
+                stdinPipe.Writer.Complete();
+                stdoutPipe.Writer.Complete();
+            }
+        }
+    }
+
     [Fact]
     public async Task Can_Be_Notified_Of_Tool_Changes()
     {
diff --git a/tests/ModelContextProtocol.Tests/Transport/StreamClientTransport.cs b/tests/ModelContextProtocol.Tests/Transport/StreamClientTransport.cs
index a8014e3..49c7ca7 100644
--- a/tests/ModelContextProtocol.Tests/Transport/StreamClientTransport.cs
+++ b/tests/ModelContextProtocol.Tests/Transport/StreamClientTransport.cs
@@ -9,16 +9,16 @@ namespace ModelContextProtocol.Tests.Transport;
 internal sealed class StreamClientTransport : TransportBase, IClientTransport
 {
     private readonly JsonSerializerOptions _jsonOptions = McpJsonUtilities.DefaultOptions;
-    private Task? _readTask;
-    private CancellationTokenSource _shutdownCts = new CancellationTokenSource();
-    private readonly TextReader _stdin;
-    private readonly TextWriter _stdout;
+    private readonly Task? _readTask;
+    private readonly CancellationTokenSource _shutdownCts = new CancellationTokenSource();
+    private readonly TextReader _serverStdoutReader;
+    private readonly TextWriter _serverStdinWriter;
 
-    public StreamClientTransport(TextReader stdin, TextWriter stdout)
+    public StreamClientTransport(TextWriter serverStdinWriter, TextReader serverStdoutReader)
         : base(NullLoggerFactory.Instance)
     {
-        _stdin = stdin;
-        _stdout = stdout;
+        _serverStdoutReader = serverStdoutReader;
+        _serverStdinWriter = serverStdinWriter;
         _readTask = Task.Run(() => ReadMessagesAsync(_shutdownCts.Token), CancellationToken.None);
         SetConnected(true);
     }
@@ -31,13 +31,13 @@ internal sealed class StreamClientTransport : TransportBase, IClientTransport
             messageWithId.Id.ToString() :
             "(no id)";
      
-        await _stdout.WriteLineAsync(JsonSerializer.Serialize(message)).ConfigureAwait(false);
-        await _stdout.FlushAsync(cancellationToken).ConfigureAwait(false);
+        await _serverStdinWriter.WriteLineAsync(JsonSerializer.Serialize(message)).ConfigureAwait(false);
+        await _serverStdinWriter.FlushAsync(cancellationToken).ConfigureAwait(false);
     }
 
     private async Task ReadMessagesAsync(CancellationToken cancellationToken)
     {
-        while (await _stdin.ReadLineAsync(cancellationToken).ConfigureAwait(false) is string line)
+        while (await _serverStdoutReader.ReadLineAsync(cancellationToken).ConfigureAwait(false) is string line)
         {
             if (!string.IsNullOrWhiteSpace(line))
             {