diff --git a/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/WebSocketConfiguration.java b/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/WebSocketConfiguration.java
index 2040ca95644..880bcec1d64 100644
--- a/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/WebSocketConfiguration.java
+++ b/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/WebSocketConfiguration.java
@@ -30,50 +30,87 @@ import org.eclipse.jetty.websocket.jsr356.server.deploy.ServerEndpointAnnotation
 import org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter;
 
 /**
- * WebSocket Server Configuration component
+ * WebSocket Server Configuration component. This configuration will configure a context for JSR356 Websockets if the attribute
+ * "org.eclipse.jetty.websocket.jsr356" is set to true. This attribute may be set on an individual context or on the server to affect all deployed contexts.
  */
 public class WebSocketConfiguration extends AbstractConfiguration
 {
+    public static final String ENABLE = "org.eclipse.jetty.websocket.jsr356";
     private static final Logger LOG = Log.getLogger(WebSocketConfiguration.class);
-    
+
+    /**
+     * Create a ServerContainer properly, useful for embedded application use.
+     * <p>
+     * Notably, the cometd3 project uses this.
+     * 
+     * @param context
+     *            the context to enable javax.websocket support filters on
+     * @return the ServerContainer that was created
+     */
     public static ServerContainer configureContext(ServletContextHandler context)
     {
+        LOG.debug("Configure javax.websocket for WebApp {}",context);
         WebSocketUpgradeFilter filter = WebSocketUpgradeFilter.configureContext(context);
-        
+
         // Create the Jetty ServerContainer implementation
         ServerContainer jettyContainer = new ServerContainer(filter,filter.getFactory());
         context.addBean(jettyContainer);
 
         // Store a reference to the ServerContainer per javax.websocket spec 1.0 final section 6.4 Programmatic Server Deployment
         context.setAttribute(javax.websocket.server.ServerContainer.class.getName(),jettyContainer);
-        
+
         // Store reference to DiscoveredEndpoints
         context.setAttribute(DiscoveredEndpoints.class.getName(),new DiscoveredEndpoints());
 
         return jettyContainer;
     }
 
+    public static boolean isJSR356Context(WebAppContext context)
+    {
+        Object enable = context.getAttribute(ENABLE);
+        if (enable instanceof Boolean)
+        {
+        }
+
+        enable = context.getServer().getAttribute(ENABLE);
+        if (enable instanceof Boolean)
+        {
+            return ((Boolean)enable).booleanValue();
+        }
+
+        return true;
+    }
+
     @Override
     public void configure(WebAppContext context) throws Exception
     {
-        LOG.debug("Configure javax.websocket for WebApp {}",context);
-        WebSocketConfiguration.configureContext(context);
+        if (isJSR356Context(context))
+        {
+            WebSocketConfiguration.configureContext(context);
+        }
+        else
+        {
+            LOG.debug("JSR-356 support disabled for WebApp {}",context);
+        }
     }
 
     @Override
     public void preConfigure(WebAppContext context) throws Exception
     {
-        boolean scanningAdded = false;
-        // Add the annotation scanning handlers (if annotation scanning enabled)
-        for (Configuration config : context.getConfigurations())
+        if (isJSR356Context(context))
         {
-            if (config instanceof AnnotationConfiguration)
+            boolean scanningAdded = false;
+            // Add the annotation scanning handlers (if annotation scanning enabled)
+            for (Configuration config : context.getConfigurations())
             {
-                AnnotationConfiguration annocfg = (AnnotationConfiguration)config;
-                annocfg.addDiscoverableAnnotationHandler(new ServerEndpointAnnotationHandler(context));
-                scanningAdded = true;
+                if (config instanceof AnnotationConfiguration)
+                {
+                    AnnotationConfiguration annocfg = (AnnotationConfiguration)config;
+                    annocfg.addDiscoverableAnnotationHandler(new ServerEndpointAnnotationHandler(context));
+                    scanningAdded = true;
+                }
             }
+            LOG.debug("@ServerEndpoint scanning added: {}",scanningAdded);
         }
-        LOG.debug("@ServerEndpoint scanning added: {}", scanningAdded);
     }
 }
diff --git a/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/deploy/ServerApplicationConfigListener.java b/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/deploy/ServerApplicationConfigListener.java
index 5b82dff24c3..5eebf2935f9 100644
--- a/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/deploy/ServerApplicationConfigListener.java
+++ b/jetty-websocket/javax-websocket-server-impl/src/main/java/org/eclipse/jetty/websocket/jsr356/server/deploy/ServerApplicationConfigListener.java
@@ -35,7 +35,9 @@ import javax.websocket.server.ServerEndpointConfig;
 
 import org.eclipse.jetty.util.log.Log;
 import org.eclipse.jetty.util.log.Logger;
+import org.eclipse.jetty.webapp.WebAppContext;
 import org.eclipse.jetty.websocket.jsr356.server.ServerContainer;
+import org.eclipse.jetty.websocket.jsr356.server.WebSocketConfiguration;
 import org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter;
 
 @HandlesTypes(
@@ -47,6 +49,9 @@ public class ServerApplicationConfigListener implements ServletContainerInitiali
     @Override
     public void onStartup(Set<Class<?>> c, ServletContext ctx) throws ServletException
     {
+        if (!WebSocketConfiguration.isJSR356Context(WebAppContext.getCurrentWebAppContext()))
+            return;
+        
         WebSocketUpgradeFilter filter = (WebSocketUpgradeFilter)ctx.getAttribute(WebSocketUpgradeFilter.class.getName());
         if (filter == null)
         {