diff --git a/examples/stdio-explicit-registration/server.php b/examples/stdio-explicit-registration/server.php
index e44d1ff..2189bf1 100644
--- a/examples/stdio-explicit-registration/server.php
+++ b/examples/stdio-explicit-registration/server.php
@@ -28,7 +28,7 @@
     ->addResource([SimpleHandlers::class, 'getAppVersion'], 'app://version', 'application_version', mimeType: 'text/plain')
     ->addPrompt([SimpleHandlers::class, 'greetingPrompt'], 'personalized_greeting')
     ->addResourceTemplate([SimpleHandlers::class, 'getItemDetails'], 'item://{itemId}/details', 'get_item_details', mimeType: 'application/json')
-    ->setServerCapabilities(new ServerCapabilities(
+    ->setCapabilities(new ServerCapabilities(
         tools: true,
         toolsListChanged: false,
         resources: true,
diff --git a/src/Server/Builder.php b/src/Server/Builder.php
index 39f2cb8..35f5d3f 100644
--- a/src/Server/Builder.php
+++ b/src/Server/Builder.php
@@ -75,8 +75,6 @@ final class Builder
 
     private ?string $instructions = null;
 
-    private ?ServerCapabilities $explicitCapabilities = null;
-
     /**
      * @var array<int, MethodHandlerInterface>
      */
@@ -177,9 +175,9 @@ public function setInstructions(?string $instructions): self
     /**
      * Explicitly set server capabilities. If set, this overrides automatic detection.
      */
-    public function setCapabilities(ServerCapabilities $capabilities): self
+    public function setCapabilities(ServerCapabilities $serverCapabilities): self
     {
-        $this->explicitCapabilities = $capabilities;
+        $this->serverCapabilities = $serverCapabilities;
 
         return $this;
     }
@@ -266,13 +264,6 @@ public function setDiscovery(
         return $this;
     }
 
-    public function setServerCapabilities(ServerCapabilities $serverCapabilities): self
-    {
-        $this->serverCapabilities = $serverCapabilities;
-
-        return $this;
-    }
-
     /**
      * Manually registers a tool handler.
      *
@@ -370,7 +361,7 @@ public function build(): Server
         $sessionStore = $this->sessionStore ?? new InMemorySessionStore($sessionTtl);
         $messageFactory = MessageFactory::make();
 
-        $capabilities = $this->explicitCapabilities ?? $registry->getCapabilities();
+        $capabilities = $registry->getCapabilities();
         $configuration = new Configuration($this->serverInfo, $capabilities, $this->paginationLimit, $this->instructions);
         $referenceHandler = new ReferenceHandler($container);
 
@@ -597,7 +588,8 @@ private function getHandlerDescription(\Closure|array|string $handler): string
         }
 
         if (\is_array($handler)) {
-            return \sprintf('%s::%s',
+            return \sprintf(
+                '%s::%s',
                 \is_object($handler[0]) ? $handler[0]::class : $handler[0],
                 $handler[1],
             );