diff --git a/ui/src/app/applications/components/application-sync-options/application-sync-options.tsx b/ui/src/app/applications/components/application-sync-options/application-sync-options.tsx
index 538d74455fea0..7cc24173cd36a 100644
--- a/ui/src/app/applications/components/application-sync-options/application-sync-options.tsx
+++ b/ui/src/app/applications/components/application-sync-options/application-sync-options.tsx
@@ -7,6 +7,7 @@ import './application-sync-options.scss';
 
 export const REPLACE_WARNING = `The resources will be synced using 'kubectl replace/create' command that is a potentially destructive action and might cause resources recreation.`;
 export const FORCE_WARNING = `The resources will be synced using '--force' that is a potentially destructive action and will immediately remove resources from the API and bypasses graceful deletion. Immediate deletion of some resources may result in inconsistency or data loss.`;
+export const PRUNE_ALL_WARNING = `The resources will be synced using '--prune', and all resources are marked to be pruned. Only continue if you want to delete all of the Application's resources.`;
 
 export interface ApplicationSyncOptionProps {
     options: string[];
diff --git a/ui/src/app/applications/components/application-sync-panel/application-sync-panel.tsx b/ui/src/app/applications/components/application-sync-panel/application-sync-panel.tsx
index 884cdd4eb85ff..c1a4505eeeba0 100644
--- a/ui/src/app/applications/components/application-sync-panel/application-sync-panel.tsx
+++ b/ui/src/app/applications/components/application-sync-panel/application-sync-panel.tsx
@@ -7,7 +7,14 @@ import {Consumer} from '../../../shared/context';
 import * as models from '../../../shared/models';
 import {services} from '../../../shared/services';
 import {ApplicationRetryOptions} from '../application-retry-options/application-retry-options';
-import {ApplicationManualSyncFlags, ApplicationSyncOptions, FORCE_WARNING, SyncFlags, REPLACE_WARNING} from '../application-sync-options/application-sync-options';
+import {
+    ApplicationManualSyncFlags,
+    ApplicationSyncOptions,
+    FORCE_WARNING,
+    SyncFlags,
+    REPLACE_WARNING,
+    PRUNE_ALL_WARNING
+} from '../application-sync-options/application-sync-options';
 import {ComparisonStatusIcon, getAppDefaultSource, nodeKey} from '../utils';
 
 import './application-sync-panel.scss';
@@ -57,9 +64,25 @@ export const ApplicationSyncPanel = ({application, selectedResource, hide}: {app
                             })}
                             onSubmit={async (params: any) => {
                                 setPending(true);
-                                let resources = appResources.filter((_, i) => params.resources[i]);
-                                if (resources.length === appResources.length) {
-                                    resources = null;
+                                let selectedResources = appResources.filter((_, i) => params.resources[i]);
+                                const allResourcesAreSelected = selectedResources.length === appResources.length;
+                                const syncFlags = {...params.syncFlags} as SyncFlags;
+
+                                const allRequirePruning = !selectedResources.some(resource => !resource?.requiresPruning);
+                                if (syncFlags.Prune && allRequirePruning && allResourcesAreSelected) {
+                                    const confirmed = await ctx.popup.confirm('Prune all resources?', () => (
+                                        <div>
+                                            <i className='fa fa-exclamation-triangle' style={{color: ARGO_WARNING_COLOR}} />
+                                            {PRUNE_ALL_WARNING} Are you sure you want to continue?
+                                        </div>
+                                    ));
+                                    if (!confirmed) {
+                                        setPending(false);
+                                        return;
+                                    }
+                                }
+                                if (allResourcesAreSelected) {
+                                    selectedResources = null;
                                 }
                                 const replace = params.syncOptions?.findIndex((opt: string) => opt === 'Replace=true') > -1;
                                 if (replace) {
@@ -74,7 +97,6 @@ export const ApplicationSyncPanel = ({application, selectedResource, hide}: {app
                                     }
                                 }
 
-                                const syncFlags = {...params.syncFlags} as SyncFlags;
                                 const force = syncFlags.Force || false;
 
                                 if (syncFlags.ApplyOnly) {
@@ -102,7 +124,7 @@ export const ApplicationSyncPanel = ({application, selectedResource, hide}: {app
                                         syncFlags.Prune || false,
                                         syncFlags.DryRun || false,
                                         syncStrategy,
-                                        resources,
+                                        selectedResources,
                                         params.syncOptions,
                                         params.retryStrategy
                                     );