diff --git a/frappe/desk/doctype/workspace/workspace.py b/frappe/desk/doctype/workspace/workspace.py
index df25bd1910..c45b249cf7 100644
--- a/frappe/desk/doctype/workspace/workspace.py
+++ b/frappe/desk/doctype/workspace/workspace.py
@@ -127,8 +127,6 @@ class Workspace(Document):
 	def on_trash(self):
 		if self.public and not is_workspace_manager():
 			frappe.throw(_("You need to be Workspace Manager to delete a public workspace."))
-		self.delete_desktop_icon()
-		self.delete_workspace_sidebar()
 		self.delete_from_my_workspaces()
 
 	def delete_from_my_workspaces(self):
@@ -145,25 +143,6 @@ class Workspace(Document):
 		if self.module and frappe.conf.developer_mode:
 			delete_folder(self.module, "Workspace", self.title)
 
-	def delete_desktop_icon(self):
-		if self.public:
-			desktop_icon = frappe.get_all(
-				"Desktop Icon",
-				filters=[{"link_type": "Workspace Sidebar"}, {"link_to": self.name}],
-				limit=1,
-				pluck="name",
-			)
-			if desktop_icon:
-				frappe.delete_doc("Desktop Icon", desktop_icon[0])
-
-	def delete_workspace_sidebar(self):
-		if self.public:
-			workspace_sidebar = frappe.get_all(
-				"Workspace Sidebar", filters=[{"name": self.name}], limit=1, pluck="name"
-			)
-			if workspace_sidebar:
-				frappe.delete_doc("Workspace Sidebar", workspace_sidebar[0])
-
 	@staticmethod
 	def get_module_wise_workspaces():
 		workspaces = frappe.get_all(
diff --git a/frappe/desk/doctype/workspace_sidebar/workspace_sidebar.py b/frappe/desk/doctype/workspace_sidebar/workspace_sidebar.py
index b54f0abbdd..d6390ca036 100644
--- a/frappe/desk/doctype/workspace_sidebar/workspace_sidebar.py
+++ b/frappe/desk/doctype/workspace_sidebar/workspace_sidebar.py
@@ -73,6 +73,7 @@ class WorkspaceSidebar(Document):
 		if is_workspace_manager():
 			if frappe.conf.developer_mode and self.app:
 				self.delete_file()
+			self.delete_desktop_icon()
 		else:
 			frappe.throw(_("You need to be Workspace Manager to delete a public workspace."))
 
@@ -136,6 +137,16 @@ class WorkspaceSidebar(Document):
 		if counts and counts.most_common(1)[0]:
 			return counts.most_common(1)[0][0]
 
+	def delete_desktop_icon(self):
+		desktop_icon = frappe.get_all(
+			"Desktop Icon",
+			filters=[{"link_type": "Workspace Sidebar"}, {"link_to": self.name}],
+			limit=1,
+			pluck="name",
+		)
+		if desktop_icon:
+			frappe.delete_doc("Desktop Icon", desktop_icon[0])
+
 	def get_allowed_modules(self):
 		if not self.user.allow_modules:
 			self.user.build_permissions()
diff --git a/frappe/desktop_icon/productivity.json b/frappe/desktop_icon/productivity.json
deleted file mode 100644
index 41c104514c..0000000000
--- a/frappe/desktop_icon/productivity.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
- "app": "frappe",
- "creation": "2025-11-25 13:27:21.246918",
- "docstatus": 0,
- "doctype": "Desktop Icon",
- "hidden": 0,
- "icon": "folder-open",
- "icon_type": "Link",
- "idx": 0,
- "label": "Productivity",
- "link_to": "Productivity",
- "link_type": "Workspace Sidebar",
- "modified": "2026-01-01 20:07:01.152305",
- "modified_by": "Administrator",
- "name": "Productivity",
- "owner": "Administrator",
- "parent_icon": "Framework",
- "restrict_removal": 0,
- "roles": [],
- "standard": 1
-}
diff --git a/frappe/model/sync.py b/frappe/model/sync.py
index 19568ca8e4..73cf16a616 100644
--- a/frappe/model/sync.py
+++ b/frappe/model/sync.py
@@ -201,13 +201,16 @@ def remove_orphan_doctypes():
 
 def remove_orphan_entities():
 	entites = ["Workspace", "Dashboard", "Page", "Report"]
+	app_level_entities = ["Workspace Sidebar"]
 	entity_filter_map = {
 		"Workspace": {"public": 1},
 		"Page": {"standard": "Yes"},
 		"Report": {"is_standard": "Yes"},
 		"Dashboard": {"is_standard": True},
+		"Workspace Sidebar": {"standard": True},
 	}
 	entity_file_map = create_entity_file_map(entites)
+
 	for entity in entites:
 		print(f"Removing orphan {entity}s")
 		all_enitities = frappe.get_all(
@@ -228,6 +231,26 @@ def remove_orphan_entities():
 					print(e)
 		# save the deleted icons
 		frappe.db.commit()  # nosemgrep
+	#  Remove app level entities
+	for app_entity in app_level_entities:
+		print(f"Removing orphan {app_entity}s")
+		all_enitities = frappe.get_all(
+			app_entity, filters=entity_filter_map.get(app_entity), fields=["name", "app"]
+		)
+		for i, w in enumerate(all_enitities):
+			if w.app and not check_if_record_exists("app", frappe.get_app_path(w.app), app_entity, w.name):
+				try:
+					print(f"Deleting entity {app_entity} {w.name}")
+					frappe.delete_doc(app_entity, w.name, force=True, ignore_missing=True)
+					update_progress_bar(f"Deleting orphaned {app_entity}", i, len(all_enitities))
+					print()
+
+				except Exception as e:
+					print(f"Error occurred while deleting entity: {app_entity} {w.name}")
+					print(e)
+
+	# save the deleted icons
+	frappe.db.commit()  # nosemgrep
 
 
 def create_entity_file_map(entities):