diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index bbbb3c978ff..68e9eef711a 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -211,12 +211,14 @@ class PaymentReconciliation(Document):
 		if self.get("cost_center"):
 			conditions.append(jea.cost_center == self.cost_center)
 
-		dr_or_cr = (
-			"credit_in_account_currency"
-			if erpnext.get_party_account_type(self.party_type) == "Receivable"
-			else "debit_in_account_currency"
-		)
-		conditions.append(jea[dr_or_cr].gt(0))
+		account_type = erpnext.get_party_account_type(self.party_type)
+
+		if account_type == "Receivable":
+			dr_or_cr = jea.credit_in_account_currency - jea.debit_in_account_currency
+		elif account_type == "Payable":
+			dr_or_cr = jea.debit_in_account_currency - jea.credit_in_account_currency
+
+		conditions.append(dr_or_cr.gt(0))
 
 		if self.bank_cash_account:
 			conditions.append(jea.against_account.like(f"%%{self.bank_cash_account}%%"))
@@ -231,7 +233,7 @@ class PaymentReconciliation(Document):
 				je.posting_date,
 				je.remark.as_("remarks"),
 				jea.name.as_("reference_row"),
-				jea[dr_or_cr].as_("amount"),
+				dr_or_cr.as_("amount"),
 				jea.is_advance,
 				jea.exchange_rate,
 				jea.account_currency.as_("currency"),
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 37dbaef51a8..144039b794f 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -630,6 +630,16 @@ def update_reference_in_journal_entry(d, journal_entry, do_not_save=False):
 	if jv_detail.get("reference_type") in ["Sales Order", "Purchase Order"]:
 		update_advance_paid.append((jv_detail.reference_type, jv_detail.reference_name))
 
+	rev_dr_or_cr = (
+		"debit_in_account_currency"
+		if d["dr_or_cr"] == "credit_in_account_currency"
+		else "credit_in_account_currency"
+	)
+	if jv_detail.get(rev_dr_or_cr):
+		d["dr_or_cr"] = rev_dr_or_cr
+		d["allocated_amount"] = d["allocated_amount"] * -1
+		d["unadjusted_amount"] = d["unadjusted_amount"] * -1
+
 	if flt(d["unadjusted_amount"]) - flt(d["allocated_amount"]) != 0:
 		# adjust the unreconciled balance
 		amount_in_account_currency = flt(d["unadjusted_amount"]) - flt(d["allocated_amount"])