diff --git a/packages/server/src/server/server.ts b/packages/server/src/server/server.ts
index 264386806..a9d6881fc 100644
--- a/packages/server/src/server/server.ts
+++ b/packages/server/src/server/server.ts
@@ -115,19 +115,23 @@ export class Server extends Protocol<ServerContext> {
         this.setNotificationHandler('notifications/initialized', () => this.oninitialized?.());
 
         if (this._capabilities.logging) {
-            this.setRequestHandler('logging/setLevel', async (request, ctx) => {
-                const transportSessionId: string | undefined =
-                    ctx.sessionId || (ctx.http?.req?.headers.get('mcp-session-id') as string) || undefined;
-                const { level } = request.params;
-                const parseResult = parseSchema(LoggingLevelSchema, level);
-                if (parseResult.success) {
-                    this._loggingLevels.set(transportSessionId, parseResult.data);
-                }
-                return {};
-            });
+            this._registerLoggingHandler();
         }
     }
 
+    private _registerLoggingHandler(): void {
+        this.setRequestHandler('logging/setLevel', async (request, ctx) => {
+            const transportSessionId: string | undefined =
+                ctx.sessionId || (ctx.http?.req?.headers.get('mcp-session-id') as string) || undefined;
+            const { level } = request.params;
+            const parseResult = parseSchema(LoggingLevelSchema, level);
+            if (parseResult.success) {
+                this._loggingLevels.set(transportSessionId, parseResult.data);
+            }
+            return {};
+        });
+    }
+
     protected override buildContext(ctx: BaseContext, transportInfo?: MessageExtraInfo): ServerContext {
         // Only create http when there's actual HTTP transport info or auth info
         const hasHttpInfo =
@@ -188,7 +192,11 @@ export class Server extends Protocol<ServerContext> {
         if (this.transport) {
             throw new SdkError(SdkErrorCode.AlreadyConnected, 'Cannot register capabilities after connecting to transport');
         }
+        const hadLogging = !!this._capabilities.logging;
         this._capabilities = mergeCapabilities(this._capabilities, capabilities);
+        if (!hadLogging && this._capabilities.logging) {
+            this._registerLoggingHandler();
+        }
     }
 
     /**
diff --git a/test/integration/test/server.test.ts b/test/integration/test/server.test.ts
index ef7cd931e..531ec9af8 100644
--- a/test/integration/test/server.test.ts
+++ b/test/integration/test/server.test.ts
@@ -3715,3 +3715,37 @@ describe('elicitInputStream', () => {
         });
     });
 });
+
+describe('Server registerCapabilities with logging', () => {
+    test('registerCapabilities should register logging/setLevel handler', async () => {
+        const server = new Server({ name: 'test-server', version: '1.0.0' });
+        server.registerCapabilities({ logging: {} });
+
+        const client = new Client({ name: 'test-client', version: '1.0.0' });
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+
+        await server.connect(serverTransport);
+        await client.connect(clientTransport);
+
+        // logging/setLevel should succeed, not throw "Method not found"
+        await expect(client.setLoggingLevel('error')).resolves.not.toThrow();
+
+        await client.close();
+        await server.close();
+    });
+
+    test('logging in constructor capabilities should register logging/setLevel handler', async () => {
+        const server = new Server({ name: 'test-server', version: '1.0.0' }, { capabilities: { logging: {} } });
+
+        const client = new Client({ name: 'test-client', version: '1.0.0' });
+        const [clientTransport, serverTransport] = InMemoryTransport.createLinkedPair();
+
+        await server.connect(serverTransport);
+        await client.connect(clientTransport);
+
+        await expect(client.setLoggingLevel('error')).resolves.not.toThrow();
+
+        await client.close();
+        await server.close();
+    });
+});