diff --git a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ApplicationPartServiceImpl.java b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ApplicationPartServiceImpl.java
index d7eaaa26603..5a532b98bc1 100644
--- a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ApplicationPartServiceImpl.java
+++ b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ApplicationPartServiceImpl.java
@@ -131,7 +131,10 @@ public Optional<MPerspective> switchPerspective(String perspectiveId) {
 	}
 
 	private void switchPerspectiveInternal(MPerspective perspective) {
-		perspective.getParent().setSelectedElement(perspective);
+		// Only set the perspective as selected if it is still to be rendered
+		if (perspective.isToBeRendered()) {
+			perspective.getParent().setSelectedElement(perspective);
+		}
 		UIEvents.publishEvent(UIEvents.UILifeCycle.PERSPECTIVE_SWITCHED, perspective);
 	}
 
diff --git a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/CommandLineOptionModelProcessor.java b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/CommandLineOptionModelProcessor.java
index 93a5da83a3e..03583b28aa7 100644
--- a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/CommandLineOptionModelProcessor.java
+++ b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/CommandLineOptionModelProcessor.java
@@ -65,7 +65,10 @@ private void selectForcedPerspective() {
 
 		for (MPerspective persp : perspStack.getChildren()) {
 			if (persp.getElementId().equals(forcedPerspectiveId)) {
-				perspStack.setSelectedElement(persp);
+				// Only set as selected if it's to be rendered
+				if (persp.isToBeRendered()) {
+					perspStack.setSelectedElement(persp);
+				}
 				return;
 			}
 		}
diff --git a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ModelServiceImpl.java b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ModelServiceImpl.java
index 5fb2f8e0017..21baeb83c4a 100644
--- a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ModelServiceImpl.java
+++ b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/ModelServiceImpl.java
@@ -609,7 +609,10 @@ public void bringToTop(MUIElement element) {
 				element.setToBeRendered(true);
 			}
 
-			window.getParent().setSelectedElement(window);
+			// Only set the window as selected if it is still to be rendered (not being removed)
+			if (window.isToBeRendered()) {
+				window.getParent().setSelectedElement(window);
+			}
 		} else {
 			showElementInWindow(window, element);
 		}
@@ -647,7 +650,10 @@ private void showElementInWindow(MWindow window, MUIElement element) {
 
 			@SuppressWarnings("unchecked")
 			MElementContainer<MUIElement> container = (MElementContainer<MUIElement>) parent;
-			container.setSelectedElement(element);
+			// Only set as selected if the element is still to be rendered
+			if (element.isToBeRendered()) {
+				container.setSelectedElement(element);
+			}
 			if (window != parent) {
 				showElementInWindow(window, parent);
 			}
diff --git a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/PartServiceImpl.java b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/PartServiceImpl.java
index c5d66843adb..9d0607fad15 100644
--- a/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/PartServiceImpl.java
+++ b/bundles/org.eclipse.e4.ui.workbench/src/org/eclipse/e4/ui/internal/workbench/PartServiceImpl.java
@@ -616,7 +616,10 @@ public void switchPerspective(MPerspective perspective) {
 		Assert.isNotNull(perspective);
 		MWindow window = getWindow();
 		if (window != null && isInContainer(window, perspective)) {
-			perspective.getParent().setSelectedElement(perspective);
+			// Only set the perspective as selected if it is still to be rendered
+			if (perspective.isToBeRendered()) {
+				perspective.getParent().setSelectedElement(perspective);
+			}
 			List<MPart> newPerspectiveParts = modelService.findElements(perspective, null,
 					MPart.class, null);
 			// if possible, keep the same active part across perspective switches
@@ -771,7 +774,10 @@ private void activate(MPart part, boolean requiresFocus, boolean activateBranch)
 			recordStackActivation(part);
 
 			delegateBringToTop(part);
-			window.getParent().setSelectedElement(window);
+			// Only set the window as selected if it is still to be rendered (not being removed)
+			if (window.isToBeRendered()) {
+				window.getParent().setSelectedElement(window);
+			}
 
 			partActivationHistory.activate(part, activateBranch);
 
@@ -1323,7 +1329,10 @@ private void createElement(MUIElement element) {
 		parent = element.getParent();
 		if (parent != null && parent.getChildren().size() == 1) {
 			// if we're the only child, set ourselves as the selected element
-			parent.setSelectedElement(element);
+			// only if we're still to be rendered
+			if (element.isToBeRendered()) {
+				parent.setSelectedElement(element);
+			}
 		}
 	}
 
@@ -1390,7 +1399,7 @@ public void hidePart(MPart part, boolean force) {
 				MUIElement candidate = partActivationHistory.getSiblingSelectionCandidate(part);
 				candidate = candidate == null ? null
 						: candidate.getCurSharedRef() == null ? candidate : candidate.getCurSharedRef();
-				if (candidate != null && children.contains(candidate)) {
+				if (candidate != null && children.contains(candidate) && candidate.isToBeRendered()) {
 					parent.setSelectedElement(candidate);
 				} else {
 					for (MUIElement child : children) {
diff --git a/tests/org.eclipse.e4.ui.tests/src/org/eclipse/e4/ui/tests/application/EPartServiceTest.java b/tests/org.eclipse.e4.ui.tests/src/org/eclipse/e4/ui/tests/application/EPartServiceTest.java
index b443c1999a1..f401ad956c6 100644
--- a/tests/org.eclipse.e4.ui.tests/src/org/eclipse/e4/ui/tests/application/EPartServiceTest.java
+++ b/tests/org.eclipse.e4.ui.tests/src/org/eclipse/e4/ui/tests/application/EPartServiceTest.java
@@ -10100,6 +10100,39 @@ public void partVisible(MPart part) {
 
 	}
 
+	/**
+	 * Test for Bug 3509: IllegalArgumentException when exiting e4-RCP application.
+	 * This test verifies that activating a part when the window is being removed
+	 * (toBeRendered=false) doesn't throw an IllegalArgumentException.
+	 */
+	@Test
+	public void testActivatePartDuringWindowCleanup() {
+		createApplication("partId");
+
+		MWindow window = application.getChildren().get(0);
+		getEngine().createGui(window);
+
+		EPartService partService = window.getContext().get(EPartService.class);
+		MPart part = partService.findPart("partId");
+		assertNotNull(part);
+
+		// Activate the part first
+		partService.activate(part);
+		assertEquals(part, partService.getActivePart());
+
+		// Simulate window cleanup by setting toBeRendered to false
+		window.setToBeRendered(false);
+
+		// Now activate the part again - this should not throw an IllegalArgumentException
+		// even though the window is no longer toBeRendered
+		try {
+			partService.activate(part);
+			// If we reach here, the fix is working
+		} catch (IllegalArgumentException e) {
+			fail("Should not throw IllegalArgumentException when activating part during window cleanup: " + e.getMessage());
+		}
+	}
+
 	static class ExceptionListener implements IPartListener {
 
 		@Override