diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 1aefeaacf7..ed374c1eb1 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -474,10 +474,12 @@ def reconcile_against_document(args, skip_ref_details_update_for_pe=False):  # n
 
 			# update ref in advance entry
 			if voucher_type == "Journal Entry":
-				update_reference_in_journal_entry(entry, doc, do_not_save=True)
+				referenced_row = update_reference_in_journal_entry(entry, doc, do_not_save=False)
 				# advance section in sales/purchase invoice and reconciliation tool,both pass on exchange gain/loss
 				# amount and account in args
-				doc.make_exchange_gain_loss_journal(args)
+				# referenced_row is used to deduplicate gain/loss journal
+				entry.update({"referenced_row": referenced_row})
+				doc.make_exchange_gain_loss_journal([entry])
 			else:
 				update_reference_in_payment_entry(
 					entry, doc, do_not_save=True, skip_ref_details_update_for_pe=skip_ref_details_update_for_pe
@@ -627,6 +629,8 @@ def update_reference_in_journal_entry(d, journal_entry, do_not_save=False):
 	if not do_not_save:
 		journal_entry.save(ignore_permissions=True)
 
+	return new_row.name
+
 
 def update_reference_in_payment_entry(
 	d, payment_entry, do_not_save=False, skip_ref_details_update_for_pe=False
@@ -1901,6 +1905,7 @@ def create_gain_loss_journal(
 	journal_entry.company = company
 	journal_entry.posting_date = nowdate()
 	journal_entry.multi_currency = 1
+	journal_entry.is_system_generated = True
 
 	party_account_currency = frappe.get_cached_value("Account", party_account, "account_currency")
 
diff --git a/erpnext/controllers/accounts_controller.py b/erpnext/controllers/accounts_controller.py
index 1d50639043..a4c81c32a2 100644
--- a/erpnext/controllers/accounts_controller.py
+++ b/erpnext/controllers/accounts_controller.py
@@ -1023,6 +1023,44 @@ class AccountsController(TransactionBase):
 				)
 			)
 
+	def gain_loss_journal_already_booked(
+		self,
+		gain_loss_account,
+		exc_gain_loss,
+		ref2_dt,
+		ref2_dn,
+		ref2_detail_no,
+	) -> bool:
+		"""
+		Check if gain/loss is booked
+		"""
+		if res := frappe.db.get_all(
+			"Journal Entry Account",
+			filters={
+				"docstatus": 1,
+				"account": gain_loss_account,
+				"reference_type": ref2_dt,  # this will be Journal Entry
+				"reference_name": ref2_dn,
+				"reference_detail_no": ref2_detail_no,
+			},
+			pluck="parent",
+		):
+			# deduplicate
+			res = list({x for x in res})
+			if exc_vouchers := frappe.db.get_all(
+				"Journal Entry",
+				filters={"name": ["in", res], "voucher_type": "Exchange Gain Or Loss"},
+				fields=["voucher_type", "total_debit", "total_credit"],
+			):
+				booked_voucher = exc_vouchers[0]
+				if (
+					booked_voucher.total_debit == exc_gain_loss
+					and booked_voucher.total_credit == exc_gain_loss
+					and booked_voucher.voucher_type == "Exchange Gain Or Loss"
+				):
+					return True
+		return False
+
 	def make_exchange_gain_loss_journal(self, args: dict = None) -> None:
 		"""
 		Make Exchange Gain/Loss journal for Invoices and Payments
@@ -1051,27 +1089,34 @@ class AccountsController(TransactionBase):
 
 							reverse_dr_or_cr = "debit" if dr_or_cr == "credit" else "credit"
 
-							je = create_gain_loss_journal(
-								self.company,
-								arg.get("party_type"),
-								arg.get("party"),
-								party_account,
+							if not self.gain_loss_journal_already_booked(
 								gain_loss_account,
 								difference_amount,
-								dr_or_cr,
-								reverse_dr_or_cr,
-								arg.get("against_voucher_type"),
-								arg.get("against_voucher"),
-								arg.get("idx"),
 								self.doctype,
 								self.name,
-								arg.get("idx"),
-							)
-							frappe.msgprint(
-								_("Exchange Gain/Loss amount has been booked through {0}").format(
-									get_link_to_form("Journal Entry", je)
+								arg.get("referenced_row"),
+							):
+								je = create_gain_loss_journal(
+									self.company,
+									arg.get("party_type"),
+									arg.get("party"),
+									party_account,
+									gain_loss_account,
+									difference_amount,
+									dr_or_cr,
+									reverse_dr_or_cr,
+									arg.get("against_voucher_type"),
+									arg.get("against_voucher"),
+									arg.get("idx"),
+									self.doctype,
+									self.name,
+									arg.get("referenced_row"),
+								)
+								frappe.msgprint(
+									_("Exchange Gain/Loss amount has been booked through {0}").format(
+										get_link_to_form("Journal Entry", je)
+									)
 								)
-							)
 
 			if self.get("doctype") == "Payment Entry":
 				# For Payment Entry, exchange_gain_loss field in the `references` table is the trigger for journal creation