diff --git a/erpnext/accounts/doctype/payment_request/payment_request.py b/erpnext/accounts/doctype/payment_request/payment_request.py
index 14a438d426d8d5fa11f66634d414c703c6c1c705..a135d248edcbe41a9a87536310f95bc6ce37e4ec 100644
--- a/erpnext/accounts/doctype/payment_request/payment_request.py
+++ b/erpnext/accounts/doctype/payment_request/payment_request.py
@@ -442,23 +442,26 @@ class PaymentRequest(Document):
 
 	@frappe.whitelist()
 	def set_as_paid(self, reference_no=None):
+		payment_entry = None
 		if reference_no and (
 			existing_pe := frappe.db.get_value(
 				"Payment Entry", filters={"docstatus": 1, "reference_no": reference_no}
 			)
 		):
-			return frappe.get_doc("Payment Entry", existing_pe)
+			payment_entry = frappe.get_doc("Payment Entry", existing_pe)
 
-		frappe.flags.mute_messages = True
-		if reference_no:
-			self.register_customer(reference_no)
+		if not payment_entry:
+			frappe.flags.mute_messages = True
+			if reference_no:
+				self.register_customer(reference_no)
 
-		payment_entry = self.create_payment_entry(reference_no=reference_no)
-		if self.make_sales_invoice:
-			self.make_invoice()
-		frappe.flags.mute_messages = False
+			payment_entry = self.create_payment_entry(reference_no=reference_no)
+			if self.make_sales_invoice:
+				self.make_invoice()
+			frappe.flags.mute_messages = False
 
-		self.db_set("status", "Paid", commit=True)
+		if self.status != "Paid":
+			self.db_set("status", "Paid", commit=True)
 
 		return payment_entry
 
@@ -724,7 +727,6 @@ class PaymentRequest(Document):
 		PAID_STATUSES = ("Authorized", "Completed", "Paid")
 		curr_status, next_status = self.status, status
 		is_not_draft = not self.docstatus.is_draft()
-
 		if next_status in PAID_STATUSES:
 			self.run_method("set_as_paid", reference_no)
 		elif (curr_status == "Requested") and (next_status == "Pending") and is_not_draft: