diff --git a/mcp/features.go b/mcp/features.go
index 1777b33f..43c58854 100644
--- a/mcp/features.go
+++ b/mcp/features.go
@@ -66,6 +66,9 @@ func (s *featureSet[T]) get(uid string) (T, bool) {
 	return t, ok
 }
 
+// len returns the number of features in the set.
+func (s *featureSet[T]) len() int { return len(s.features) }
+
 // all returns an iterator over of all the features in the set
 // sorted by unique ID.
 func (s *featureSet[T]) all() iter.Seq[T] {
diff --git a/mcp/server.go b/mcp/server.go
index f9b76539..16cc8d6b 100644
--- a/mcp/server.go
+++ b/mcp/server.go
@@ -204,6 +204,26 @@ func (s *Server) RemoveResourceTemplates(uriTemplates ...string) {
 		func() bool { return s.resourceTemplates.remove(uriTemplates...) })
 }
 
+func (s *Server) capabilities() *serverCapabilities {
+	s.mu.Lock()
+	defer s.mu.Unlock()
+
+	caps := &serverCapabilities{
+		Completions: &completionCapabilities{},
+		Logging:     &loggingCapabilities{},
+	}
+	if s.tools.len() > 0 {
+		caps.Tools = &toolCapabilities{ListChanged: true}
+	}
+	if s.prompts.len() > 0 {
+		caps.Prompts = &promptCapabilities{ListChanged: true}
+	}
+	if s.resources.len() > 0 || s.resourceTemplates.len() > 0 {
+		caps.Resources = &resourceCapabilities{ListChanged: true}
+	}
+	return caps
+}
+
 func (s *Server) complete(ctx context.Context, ss *ServerSession, params *CompleteParams) (Result, error) {
 	if s.opts.CompletionHandler == nil {
 		return nil, jsonrpc2.ErrMethodNotFound
@@ -407,6 +427,11 @@ func fileResourceHandler(dir string) ResourceHandler {
 //
 // Run blocks until the client terminates the connection or the provided
 // context is cancelled. If the context is cancelled, Run closes the connection.
+//
+// If tools have been added to the server before this call, then the server will
+// advertise the capability for tools, including the ability to send list-changed notifications.
+// If no tools have been added, the server will not have the tool capability.
+// The same goes for other features like prompts and resources.
 func (s *Server) Run(ctx context.Context, t Transport) error {
 	ss, err := s.Connect(ctx, t)
 	if err != nil {
@@ -659,20 +684,8 @@ func (ss *ServerSession) initialize(ctx context.Context, params *InitializeParam
 		// TODO(rfindley): alter behavior when falling back to an older version:
 		// reject unsupported features.
 		ProtocolVersion: version,
-		Capabilities: &serverCapabilities{
-			Completions: &completionCapabilities{},
-			Prompts: &promptCapabilities{
-				ListChanged: true,
-			},
-			Tools: &toolCapabilities{
-				ListChanged: true,
-			},
-			Resources: &resourceCapabilities{
-				ListChanged: true,
-			},
-			Logging: &loggingCapabilities{},
-		},
-		Instructions: ss.server.opts.Instructions,
+		Capabilities:    ss.server.capabilities(),
+		Instructions:    ss.server.opts.Instructions,
 		ServerInfo: &implementation{
 			Name:    ss.server.name,
 			Version: ss.server.version,
diff --git a/mcp/server_test.go b/mcp/server_test.go
index 19701f39..cc94003c 100644
--- a/mcp/server_test.go
+++ b/mcp/server_test.go
@@ -227,3 +227,91 @@ func TestServerPaginateVariousPageSizes(t *testing.T) {
 		}
 	}
 }
+
+func TestServerCapabilities(t *testing.T) {
+	testCases := []struct {
+		name             string
+		configureServer  func(s *Server)
+		wantCapabilities *serverCapabilities
+	}{
+		{
+			name:            "No capabilities",
+			configureServer: func(s *Server) {},
+			wantCapabilities: &serverCapabilities{
+				Completions: &completionCapabilities{},
+				Logging:     &loggingCapabilities{},
+			},
+		},
+		{
+			name: "With prompts",
+			configureServer: func(s *Server) {
+				s.AddPrompt(&Prompt{Name: "p"}, nil)
+			},
+			wantCapabilities: &serverCapabilities{
+				Completions: &completionCapabilities{},
+				Logging:     &loggingCapabilities{},
+				Prompts:     &promptCapabilities{ListChanged: true},
+			},
+		},
+		{
+			name: "With resources",
+			configureServer: func(s *Server) {
+				s.AddResource(&Resource{URI: "file:///r"}, nil)
+			},
+			wantCapabilities: &serverCapabilities{
+				Completions: &completionCapabilities{},
+				Logging:     &loggingCapabilities{},
+				Resources:   &resourceCapabilities{ListChanged: true},
+			},
+		},
+		{
+			name: "With resource templates",
+			configureServer: func(s *Server) {
+				s.AddResourceTemplate(&ResourceTemplate{URITemplate: "file:///rt"}, nil)
+			},
+			wantCapabilities: &serverCapabilities{
+				Completions: &completionCapabilities{},
+				Logging:     &loggingCapabilities{},
+				Resources:   &resourceCapabilities{ListChanged: true},
+			},
+		},
+		{
+			name: "With tools",
+			configureServer: func(s *Server) {
+				s.AddTool(&Tool{Name: "t"}, nil)
+			},
+			wantCapabilities: &serverCapabilities{
+				Completions: &completionCapabilities{},
+				Logging:     &loggingCapabilities{},
+				Tools:       &toolCapabilities{ListChanged: true},
+			},
+		},
+		{
+			name: "With all capabilities",
+			configureServer: func(s *Server) {
+				s.AddPrompt(&Prompt{Name: "p"}, nil)
+				s.AddResource(&Resource{URI: "file:///r"}, nil)
+				s.AddResourceTemplate(&ResourceTemplate{URITemplate: "file:///rt"}, nil)
+				s.AddTool(&Tool{Name: "t"}, nil)
+			},
+			wantCapabilities: &serverCapabilities{
+				Completions: &completionCapabilities{},
+				Logging:     &loggingCapabilities{},
+				Prompts:     &promptCapabilities{ListChanged: true},
+				Resources:   &resourceCapabilities{ListChanged: true},
+				Tools:       &toolCapabilities{ListChanged: true},
+			},
+		},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.name, func(t *testing.T) {
+			server := NewServer("", "", nil)
+			tc.configureServer(server)
+			gotCapabilities := server.capabilities()
+			if diff := cmp.Diff(tc.wantCapabilities, gotCapabilities); diff != "" {
+				t.Errorf("capabilities() mismatch (-want +got):\n%s", diff)
+			}
+		})
+	}
+}
diff --git a/mcp/streamable_test.go b/mcp/streamable_test.go
index 412d2e1d..da9c4285 100644
--- a/mcp/streamable_test.go
+++ b/mcp/streamable_test.go
@@ -159,8 +159,6 @@ func TestStreamableServerTransport(t *testing.T) {
 		Capabilities: &serverCapabilities{
 			Completions: &completionCapabilities{},
 			Logging:     &loggingCapabilities{},
-			Prompts:     &promptCapabilities{ListChanged: true},
-			Resources:   &resourceCapabilities{ListChanged: true},
 			Tools:       &toolCapabilities{ListChanged: true},
 		},
 		ProtocolVersion: latestProtocolVersion,