diff --git a/frappe/core/doctype/domain/domain.py b/frappe/core/doctype/domain/domain.py
index 1fe3a967c1..61869f8fe8 100644
--- a/frappe/core/doctype/domain/domain.py
+++ b/frappe/core/doctype/domain/domain.py
@@ -18,10 +18,11 @@ class Domain(Document):
 		self.setup_roles()
 		self.setup_properties()
 		self.set_values()
-		if not int(frappe.db.get_single_value('System Settings', 'setup_complete') or 0):
+		# always set the desktop icons while changing the domain settings
+		self.setup_desktop_icons()
+		if not int(frappe.defaults.get_defaults().setup_complete or 0):
 			# if setup not complete, setup desktop etc.
 			self.setup_sidebar_items()
-			self.setup_desktop_icons()
 			self.set_default_portal_role()
 
 		if self.data.custom_fields:
diff --git a/frappe/core/doctype/domain_settings/domain_settings.py b/frappe/core/doctype/domain_settings/domain_settings.py
index ab3cfc38df..2ac9c716a7 100644
--- a/frappe/core/doctype/domain_settings/domain_settings.py
+++ b/frappe/core/doctype/domain_settings/domain_settings.py
@@ -15,7 +15,10 @@ class DomainSettings(Document):
 		self.save()
 
 	def on_update(self):
-		for d in self.active_domains:
+		for i, d in enumerate(self.active_domains):
+			# set the flag to update the the desktop icons of all domains
+			if i >= 1:
+				frappe.flags.keep_desktop_icons = True
 			domain = frappe.get_doc('Domain', d.domain)
 			domain.setup_domain()
 
diff --git a/frappe/desk/doctype/desktop_icon/desktop_icon.py b/frappe/desk/doctype/desktop_icon/desktop_icon.py
index 91de421e8f..6d5e2d6ab5 100644
--- a/frappe/desk/doctype/desktop_icon/desktop_icon.py
+++ b/frappe/desk/doctype/desktop_icon/desktop_icon.py
@@ -196,11 +196,13 @@ def set_desktop_icons(visible_list, ignore_duplicate=True):
 	if the desktop icon does not exist and the name is a DocType, then will create
 	an icon for the doctype'''
 
-	# clear all custom
-	frappe.db.sql('delete from `tabDesktop Icon` where standard=0')
+	# clear all custom only if setup is not complete
+	if not int(frappe.defaults.get_defaults().setup_complete or 0):
+		frappe.db.sql('delete from `tabDesktop Icon` where standard=0')
 
-	# set all as blocked
-	frappe.db.sql('update `tabDesktop Icon` set blocked=0, hidden=1')
+	# set standard as blocked and hidden if setting first active domain
+	if not frappe.flags.keep_desktop_icons:
+		frappe.db.sql('update `tabDesktop Icon` set blocked=0, hidden=1 where standard=1')
 
 	# set as visible if present, or add icon
 	for module_name in visible_list: