diff --git a/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/WindowsDefenderConfigurator.java b/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/WindowsDefenderConfigurator.java
index 10d87544798..135aac4a201 100644
--- a/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/WindowsDefenderConfigurator.java	
+++ b/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/WindowsDefenderConfigurator.java	
@@ -240,7 +240,11 @@ public static IEclipsePreferences getPreference(IScopeContext instance) {
 
 	public static void savePreference(IScopeContext scope, String key, String value) throws CoreException {
 		IEclipsePreferences preferences = getPreference(scope);
-		preferences.put(key, value);
+		if (value != null) {
+			preferences.put(key, value);
+		} else {
+			preferences.remove(key);
+		}
 		try {
 			preferences.flush();
 		} catch (BackingStoreException e) {
diff --git a/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/dialogs/StartupPreferencePage.java b/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/dialogs/StartupPreferencePage.java
index 58a290a16b2..aa856feccb7 100644
--- a/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/dialogs/StartupPreferencePage.java	
+++ b/bundles/org.eclipse.ui.workbench/Eclipse UI/org/eclipse/ui/internal/dialogs/StartupPreferencePage.java	
@@ -237,7 +237,8 @@ public boolean performOk() {
 
 		windowsDefenderIgnore.forEach((scope, button) -> {
 			try {
-				String skip = Boolean.toString(button.getSelection());
+				// If disabled remove the node to allow higher-level scopes to be considered
+				String skip = button.getSelection() ? Boolean.TRUE.toString() : null;
 				WindowsDefenderConfigurator.savePreference(scope, PREFERENCE_STARTUP_CHECK_SKIP, skip);
 			} catch (CoreException e) {
 				WorkbenchPlugin.log("Failed to save Windows Defender exclusion check preferences", e); //$NON-NLS-1$