diff --git a/frappe/desk/notifications.py b/frappe/desk/notifications.py
index 995c16154c..5aa9f0a40e 100644
--- a/frappe/desk/notifications.py
+++ b/frappe/desk/notifications.py
@@ -2,6 +2,7 @@
 # License: MIT. See LICENSE
 
 import json
+from typing import Literal
 
 from bs4 import BeautifulSoup
 
@@ -251,6 +252,18 @@ def get_open_count(doctype: str, name: str, items=None):
 	if frappe.flags.in_migrate or frappe.flags.in_install:
 		return {"count": []}
 
+	# None of the count queries should take more than 1s individually
+	frappe.db.set_execution_timeout(1)
+
+	try:
+		return _get_linked_document_counts(doctype, name, items)
+	except Exception as e:
+		if frappe.db.is_statement_timeout(e):
+			return {"count": []}
+		raise
+
+
+def _get_linked_document_counts(doctype: str, name: str, items=None):
 	doc = frappe.get_lazy_doc(doctype, name)
 	doc.check_permission()
 	meta = doc.meta
@@ -342,18 +355,16 @@ def get_external_links(doctype, name, links):
 	return {"doctype": doctype, "count": total_count, "open_count": open_count}
 
 
-def get_doc_count(doctype, filters):
-	return len(
-		frappe.get_all(
-			doctype,
-			fields="name",
-			filters=filters,
-			limit=100,
-			distinct=True,
-			ignore_ifnull=True,
-			order_by=None,
+def get_doc_count(doctype, filters) -> int | Literal["?"]:
+	try:
+		docs = frappe.get_all(
+			doctype, filters=filters, limit=100, distinct=True, ignore_ifnull=True, order_by=None
 		)
-	)
+		return len(docs)
+	except Exception as e:
+		if frappe.db.is_statement_timeout(e):  # Skip fetching correct count if it's too slow
+			return "?"
+		raise
 
 
 def get_dynamic_link_filters(doctype, links, fieldname):
diff --git a/frappe/public/js/frappe/form/dashboard.js b/frappe/public/js/frappe/form/dashboard.js
index f381543231..ddb8ba2e02 100644
--- a/frappe/public/js/frappe/form/dashboard.js
+++ b/frappe/public/js/frappe/form/dashboard.js
@@ -457,18 +457,14 @@ frappe.ui.form.Dashboard = class FormDashboard {
 		$.each(count.internal_links_found, function (i, d) {
 			me.frm.dashboard.set_badge_count_for_internal_link(
 				d.doctype,
-				cint(d.open_count),
-				cint(d.count),
+				d.open_count,
+				d.count,
 				d.names
 			);
 		});
 
 		$.each(count.external_links_found, function (i, d) {
-			me.frm.dashboard.set_badge_count_for_external_link(
-				d.doctype,
-				cint(d.open_count),
-				cint(d.count)
-			);
+			me.frm.dashboard.set_badge_count_for_external_link(d.doctype, d.open_count, d.count);
 		});
 	}
 
@@ -499,14 +495,20 @@ frappe.ui.form.Dashboard = class FormDashboard {
 			$link
 				.find(".open-notification")
 				.removeClass("hidden")
-				.html(open_count > 99 ? "99+" : open_count);
+				.html(cint(open_count) > 99 ? "99+" : open_count);
 		}
 
 		if (count) {
 			$link
 				.find(".count")
 				.removeClass("hidden")
-				.text(count > 99 ? "99+" : count);
+				.text(cint(count) > 99 ? "99+" : count)
+				.attr(
+					"title",
+					count != "?"
+						? __("Count of linked documents")
+						: __("Accurate count can not be fetched, click here to view all documents")
+				);
 		}
 	}