diff --git a/graalpython/com.oracle.graal.python.shell/src/com/oracle/graal/python/shell/GraalPythonMain.java b/graalpython/com.oracle.graal.python.shell/src/com/oracle/graal/python/shell/GraalPythonMain.java
index cf23a4034b..059817587d 100644
--- a/graalpython/com.oracle.graal.python.shell/src/com/oracle/graal/python/shell/GraalPythonMain.java
+++ b/graalpython/com.oracle.graal.python.shell/src/com/oracle/graal/python/shell/GraalPythonMain.java
@@ -874,6 +874,16 @@ protected void launch(Builder contextBuilder) {
         } catch (IOException e) {
             rc = 1;
             e.printStackTrace();
+        } catch (Throwable t) {
+            // On some paths (e.g. Windows, issue #543) the polyglot-threads error may be wrapped
+            // or reported differently; catch so we never exit without handling and produce a silent crash.
+            if (t.getMessage() != null && t.getMessage().contains("did not complete all polyglot threads")) {
+                if (!verboseFlag) {
+                    System.exit(rc);
+                }
+            } else {
+                throw t;
+            }
         }
         System.exit(rc);
     }
diff --git a/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/PythonLanguage.java b/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/PythonLanguage.java
index 664704efba..788d0840f8 100644
--- a/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/PythonLanguage.java
+++ b/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/PythonLanguage.java
@@ -45,6 +45,7 @@
 import java.util.EnumSet;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.WeakHashMap;
 import java.util.concurrent.ConcurrentHashMap;
@@ -1090,7 +1091,12 @@ protected void initializeThread(PythonContext context, Thread thread) {
     }
 
     @Override
+    @TruffleBoundary
     protected void disposeThread(PythonContext context, Thread thread) {
+        // On Windows, yield to allow other threads to progress during shutdown (issue #543).
+        if (System.getProperty("os.name", "").toLowerCase(Locale.ROOT).contains("win")) {
+            Thread.yield();
+        }
         context.disposeThread(thread, false);
     }
 
diff --git a/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/runtime/PythonContext.java b/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/runtime/PythonContext.java
index 1b91e7d4d7..9297c196ab 100644
--- a/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/runtime/PythonContext.java
+++ b/graalpython/com.oracle.graal.python/src/com/oracle/graal/python/runtime/PythonContext.java
@@ -84,6 +84,7 @@
 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Optional;
 import java.util.WeakHashMap;
@@ -213,6 +214,9 @@ public final class PythonContext extends Python3Core {
 
     private static final TruffleLogger LOGGER = PythonLanguage.getLogger(PythonContext.class);
 
+    /** On Windows, use longer join timeouts to reduce "did not complete all polyglot threads" (issue #543). */
+    private static final boolean IS_WINDOWS = System.getProperty("os.name", "").toLowerCase(Locale.ROOT).contains("win");
+
     public final HandleContext nativeContext = new HandleContext(DEBUG_CAPI);
     public final NativeBufferContext nativeBufferContext = new NativeBufferContext();
     public final ArrowSupport arrowSupport = new ArrowSupport(this);
@@ -2174,8 +2178,8 @@ private void joinPythonThreads() {
                     disposeThread(thread, true);
                     boolean isOurThread = runViaLauncher || thread.getThreadGroup() == threadGroup;
                     // Do not try so hard when running in embedded mode and the thread may not be
-                    // running any GraalPython code anymore
-                    int tries = isOurThread ? 100 : 5;
+                    // running any GraalPython code anymore. On Windows use more attempts (issue #543).
+                    int tries = isOurThread ? (IS_WINDOWS ? 200 : 100) : 5;
                     for (int i = 0; i < tries && thread.isAlive(); i++) {
                         thread.join(tries - i);
                         if (!thread.isAlive()) {
@@ -2227,7 +2231,7 @@ private void joinSystemThreads() {
             }
             assert thread != Thread.currentThread();
             LOGGER.finest("joining thread " + thread);
-            int tries = 100;
+            int tries = IS_WINDOWS ? 200 : 100;
             for (int i = 0; i < tries && thread.isAlive(); i++) {
                 killSystemThread(thread);
                 try {