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 293e34d2a6873..6bf9190122b4e 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
@@ -7,14 +7,7 @@ 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,
-    PRUNE_WARNING
-} from '../application-sync-options/application-sync-options';
+import {ApplicationManualSyncFlags, ApplicationSyncOptions, FORCE_WARNING, SyncFlags, REPLACE_WARNING, PRUNE_WARNING} from '../application-sync-options/application-sync-options';
 import {ComparisonStatusIcon, getAppDefaultSource, nodeKey} from '../utils';
 
 import './application-sync-panel.scss';
@@ -65,6 +58,24 @@ export const ApplicationSyncPanel = ({application, selectedResource, hide}: {app
                             onSubmit={async (params: any) => {
                                 setPending(true);
                                 let resources = appResources.filter((_, i) => params.resources[i]);
+
+                                const syncFlags = {...params.syncFlags} as SyncFlags;
+                                const prune = syncFlags.Prune || false;
+                                const requiresPrune = resources.filter(resource => resource?.requiresPruning === true);
+
+                                if (prune && appResources.length === requiresPrune.length) {
+                                    const confirmed = await ctx.popup.confirm('Synchronize with prune?', () => (
+                                        <div>
+                                            <i className='fa fa-exclamation-triangle' style={{color: ARGO_WARNING_COLOR}} />
+                                            {PRUNE_WARNING} Are you sure you want to continue?
+                                        </div>
+                                    ));
+                                    if (!confirmed) {
+                                        setPending(false);
+                                        return;
+                                    }
+                                }
+
                                 if (resources.length === appResources.length) {
                                     resources = null;
                                 }
@@ -81,9 +92,7 @@ export const ApplicationSyncPanel = ({application, selectedResource, hide}: {app
                                     }
                                 }
 
-                                const syncFlags = {...params.syncFlags} as SyncFlags;
                                 const force = syncFlags.Force || false;
-                                const prune = syncFlags.Prune || false;
 
                                 if (syncFlags.ApplyOnly) {
                                     syncStrategy.apply = {force};
@@ -101,19 +110,6 @@ export const ApplicationSyncPanel = ({application, selectedResource, hide}: {app
                                         return;
                                     }
                                 }
-                                if (prune) {
-                                    const confirmed = await ctx.popup.confirm('Synchronize with prune?', () => (
-                                        <div>
-                                            <i className='fa fa-exclamation-triangle'
-                                               style={{color: ARGO_WARNING_COLOR}}/> {PRUNE_WARNING} Are you sure you
-                                            want to continue?
-                                        </div>
-                                    ));
-                                    if (!confirmed) {
-                                        setPending(false);
-                                        return;
-                                    }
-                                }
 
                                 try {
                                     await services.applications.sync(