diff --git a/core/src/main/java/hudson/WebAppMain.java b/core/src/main/java/hudson/WebAppMain.java
index 11d438d5ab..d3375be646 100644
--- a/core/src/main/java/hudson/WebAppMain.java
+++ b/core/src/main/java/hudson/WebAppMain.java
@@ -396,8 +396,10 @@ public class WebAppMain implements ServletContextListener {
         if(instance!=null)
             instance.cleanUp();
         Thread t = initThread;
-        if (t!=null)
+        if (t != null && t.isAlive()) {
+            LOGGER.log(Level.INFO, "Shutting down a Jenkins instance that was still starting up", new Throwable("reason"));
             t.interrupt();
+        }
 
         // Logger is in the system classloader, so if we don't do this
         // the whole web app will never be undepoyed.