diff --git a/pkg/sync/sync_context.go b/pkg/sync/sync_context.go
index 8f4d51e4f..86dda5a7f 100644
--- a/pkg/sync/sync_context.go
+++ b/pkg/sync/sync_context.go
@@ -115,6 +115,13 @@ func WithPrune(prune bool) SyncOpt {
 	}
 }
 
+// WithRequiresPruneConfirmation specifies if pruning resources requires a confirmation
+func WithRequiresPruneConfirmation(requiresConfirmation bool) SyncOpt {
+	return func(ctx *syncContext) {
+		ctx.requiresPruneConfirmation = requiresConfirmation
+	}
+}
+
 // WithPruneConfirmed specifies if prune is confirmed for resources that require confirmation
 func WithPruneConfirmed(confirmed bool) SyncOpt {
 	return func(ctx *syncContext) {
@@ -122,6 +129,13 @@ func WithPruneConfirmed(confirmed bool) SyncOpt {
 	}
 }
 
+// WithPruneDisabled specifies if prune is globally disabled for this application
+func WithPruneDisabled(disabled bool) SyncOpt {
+	return func(ctx *syncContext) {
+		ctx.pruneDisabled = disabled
+	}
+}
+
 // WithOperationSettings allows to set sync operation settings
 func WithOperationSettings(dryRun bool, prune bool, force bool, skipHooks bool) SyncOpt {
 	return func(ctx *syncContext) {
@@ -367,6 +381,8 @@ type syncContext struct {
 	pruneLast                       bool
 	prunePropagationPolicy          *metav1.DeletionPropagation
 	pruneConfirmed                  bool
+	requiresPruneConfirmation       bool
+	pruneDisabled                   bool
 	clientSideApplyMigrationManager string
 	enableClientSideApplyMigration  bool
 
@@ -1212,7 +1228,7 @@ func (sc *syncContext) applyObject(t *syncTask, dryRun, validate bool) (common.R
 func (sc *syncContext) pruneObject(liveObj *unstructured.Unstructured, prune, dryRun bool) (common.ResultCode, string) {
 	if !prune {
 		return common.ResultCodePruneSkipped, "ignored (requires pruning)"
-	} else if resourceutil.HasAnnotationOption(liveObj, common.AnnotationSyncOptions, common.SyncOptionDisablePrune) {
+	} else if resourceutil.HasAnnotationOption(liveObj, common.AnnotationSyncOptions, common.SyncOptionDisablePrune) || sc.pruneDisabled {
 		return common.ResultCodePruneSkipped, "ignored (no prune)"
 	}
 	if dryRun {
@@ -1372,7 +1388,7 @@ func (sc *syncContext) runTasks(tasks syncTasks, dryRun bool) runState {
 		if !sc.pruneConfirmed {
 			var resources []string
 			for _, task := range pruneTasks {
-				if resourceutil.HasAnnotationOption(task.liveObj, common.AnnotationSyncOptions, common.SyncOptionPruneRequireConfirm) {
+				if sc.requiresPruneConfirmation || resourceutil.HasAnnotationOption(task.liveObj, common.AnnotationSyncOptions, common.SyncOptionPruneRequireConfirm) {
 					resources = append(resources, fmt.Sprintf("%s/%s/%s", task.obj().GetAPIVersion(), task.obj().GetKind(), task.name()))
 				}
 			}
diff --git a/pkg/sync/sync_context_test.go b/pkg/sync/sync_context_test.go
index 0e8d01ebb..4fd6893f1 100644
--- a/pkg/sync/sync_context_test.go
+++ b/pkg/sync/sync_context_test.go
@@ -8,6 +8,7 @@ import (
 	"net/http"
 	"net/http/httptest"
 	"reflect"
+	"strconv"
 	"strings"
 	"testing"
 	"time"
@@ -767,6 +768,60 @@ func TestDoNotPrunePruneFalse(t *testing.T) {
 
 	phase, _, _ = syncCtx.GetState()
 	assert.Equal(t, synccommon.OperationSucceeded, phase)
+
+	// test that we can still not prune if prune is disabled on the app level
+	syncCtx.pruneDisabled = true
+	pod.SetAnnotations(map[string]string{synccommon.AnnotationSyncOptions: "Prune=true"})
+	syncCtx.Sync()
+
+	phase, _, resources = syncCtx.GetState()
+
+	assert.Equal(t, synccommon.OperationSucceeded, phase)
+	assert.Len(t, resources, 1)
+	assert.Equal(t, synccommon.ResultCodePruneSkipped, resources[0].Status)
+	assert.Equal(t, "ignored (no prune)", resources[0].Message)
+
+	syncCtx.Sync()
+
+	phase, _, _ = syncCtx.GetState()
+	assert.Equal(t, synccommon.OperationSucceeded, phase)
+}
+
+// make sure that we need confirmation to prune with Prune=confirm
+func TestPruneConfirm(t *testing.T) {
+	for _, appLevelConfirmation := range []bool{true, false} {
+		t.Run("appLevelConfirmation="+strconv.FormatBool(appLevelConfirmation), func(t *testing.T) {
+			syncCtx := newTestSyncCtx(nil, WithOperationSettings(false, true, false, false))
+			syncCtx.requiresPruneConfirmation = appLevelConfirmation
+			pod := testingutils.NewPod()
+			if appLevelConfirmation {
+				pod.SetAnnotations(map[string]string{synccommon.AnnotationSyncOptions: "Prune=true"})
+			} else {
+				pod.SetAnnotations(map[string]string{synccommon.AnnotationSyncOptions: "Prune=confirm"})
+			}
+			pod.SetNamespace(testingutils.FakeArgoCDNamespace)
+			syncCtx.resources = groupResources(ReconciliationResult{
+				Live:   []*unstructured.Unstructured{pod},
+				Target: []*unstructured.Unstructured{nil},
+			})
+
+			syncCtx.Sync()
+			phase, msg, resources := syncCtx.GetState()
+
+			assert.Equal(t, synccommon.OperationRunning, phase)
+			assert.Empty(t, resources)
+			assert.Equal(t, "Waiting for pruning confirmation of v1/Pod/my-pod", msg)
+
+			syncCtx.pruneConfirmed = true
+			syncCtx.Sync()
+
+			phase, _, resources = syncCtx.GetState()
+			assert.Equal(t, synccommon.OperationSucceeded, phase)
+			assert.Len(t, resources, 1)
+			assert.Equal(t, synccommon.ResultCodePruned, resources[0].Status)
+			assert.Equal(t, "pruned", resources[0].Message)
+		})
+	}
 }
 
 // // make sure Validate=false means we don't validate