diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.js b/erpnext/accounts/doctype/payment_entry/payment_entry.js
index f8e8a6089ff8..23b8f873b5de 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.js
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.js
@@ -1087,6 +1087,8 @@ frappe.ui.form.on("Payment Entry", {
 			}
 		}
 
+		let set_matched_payment_requests = false;
+
 		$.each(frm.doc.references || [], function (i, row) {
 			if (frappe.flags.allocate_payment_amount == 0) {
 				//If allocate payment amount checkbox is unchecked, set zero to allocate amount
@@ -1095,6 +1097,8 @@ frappe.ui.form.on("Payment Entry", {
 				frappe.flags.allocate_payment_amount != 0 &&
 				(!row.allocated_amount || paid_amount_change)
 			) {
+				let previous_allocated_amount = row.allocated_amount;
+
 				if (row.outstanding_amount > 0 && allocated_positive_outstanding >= 0) {
 					row.allocated_amount =
 						row.outstanding_amount >= allocated_positive_outstanding
@@ -1108,12 +1112,16 @@ frappe.ui.form.on("Payment Entry", {
 							: row.outstanding_amount;
 					allocated_negative_outstanding -= Math.abs(flt(row.allocated_amount));
 				}
+
+				if (!row.payment_request && row.allocated_amount > previous_allocated_amount) {
+					set_matched_payment_requests = true;
+				}
 			}
 		});
 
 		frm.refresh_fields();
-		if (frappe.flags.allocate_payment_amount) frm.call("set_matched_payment_requests");
 		frm.events.set_total_allocated_amount(frm);
+		if (set_matched_payment_requests) frm.call("set_matched_payment_requests");
 	},
 
 	set_total_allocated_amount: function (frm) {
@@ -1707,7 +1715,7 @@ frappe.ui.form.on("Payment Entry Reference", {
 
 		const row = frappe.get_doc(cdt, cdn);
 
-		if (row.payment_request || !row.reference_name || !row.reference_doctype || !row.allocated_amount)
+		if (row.payment_request || !(row.reference_doctype && row.reference_name && row.allocated_amount))
 			return;
 
 		frm.call("set_matched_payment_request", { row_idx: row.idx });
diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index b08464f73f07..ef5945561c26 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -294,15 +294,17 @@ def update_outstanding_amounts(self):
 		self.set_missing_ref_details(force=True)
 
 	def validate_duplicate_entry(self):
-		reference_names = []
+		reference_names = {}
 		for d in self.get("references"):
-			if (d.reference_doctype, d.reference_name, d.payment_term) in reference_names:
+			key = (d.reference_doctype, d.reference_name, d.payment_term, d.payment_request)
+			if key in reference_names:
 				frappe.throw(
 					_("Row #{0}: Duplicate entry in References {1} {2}").format(
 						d.idx, d.reference_doctype, d.reference_name
 					)
 				)
-			reference_names.append((d.reference_doctype, d.reference_name, d.payment_term))
+
+			reference_names.add(key)
 
 	def set_bank_account_data(self):
 		if self.bank_account:
@@ -1742,10 +1744,13 @@ def check_references_for_unset_payment_request(self):
 		if not self.references:
 			return
 
-		matched_payment_requests = get_matched_payment_requests_of_references(
+		matched_payment_requests = get_matched_payment_requests(
 			[row for row in self.references if not row.payment_request]
 		)
 
+		if not matched_payment_requests:
+			return
+
 		unset_pr_rows = {}
 
 		for row in self.references:
@@ -1776,7 +1781,7 @@ def set_matched_payment_requests(self):
 		if not self.references:
 			return
 
-		matched_payment_requests = get_matched_payment_requests_of_references(self.references)
+		matched_payment_requests = get_matched_payment_requests(self.references)
 
 		matched_count = 0
 
@@ -1820,7 +1825,7 @@ def set_matched_payment_request(self, row_idx):
 		):
 			return
 
-		matched_pr = get_matched_payment_requests_of_references([row])
+		matched_pr = get_matched_payment_requests([row])
 
 		if not matched_pr:
 			return
@@ -1833,7 +1838,7 @@ def set_matched_payment_request(self, row_idx):
 		)
 
 
-def get_matched_payment_requests_of_references(references=None):
+def get_matched_payment_requests(references=None):
 	if not references:
 		return