diff --git a/erpnext/accounts/doctype/journal_entry/journal_entry.js b/erpnext/accounts/doctype/journal_entry/journal_entry.js
index b7f383f..b6c48c8 100644
--- a/erpnext/accounts/doctype/journal_entry/journal_entry.js
+++ b/erpnext/accounts/doctype/journal_entry/journal_entry.js
@@ -228,6 +228,10 @@
 				frappe.model.validate_missing(jvd, "account");
 				var party_account_field = jvd.reference_type==="Sales Invoice" ? "debit_to": "credit_to";
 				out.filters.push([jvd.reference_type, party_account_field, "=", jvd.account]);
+
+				if (in_list(['Debit Note', 'Credit Note'], doc.voucher_type)) {
+					out.filters.push([jvd.reference_type, "is_return", "=", 1]);
+				}
 			}
 
 			if(in_list(["Sales Order", "Purchase Order"], jvd.reference_type)) {
diff --git a/erpnext/accounts/doctype/journal_entry/journal_entry.py b/erpnext/accounts/doctype/journal_entry/journal_entry.py
index d082b60..3132c93 100644
--- a/erpnext/accounts/doctype/journal_entry/journal_entry.py
+++ b/erpnext/accounts/doctype/journal_entry/journal_entry.py
@@ -331,7 +331,8 @@
 		for reference_name, total in iteritems(self.reference_totals):
 			reference_type = self.reference_types[reference_name]
 
-			if reference_type in ("Sales Invoice", "Purchase Invoice"):
+			if (reference_type in ("Sales Invoice", "Purchase Invoice") and
+				self.voucher_type not in ['Debit Note', 'Credit Note']):
 				invoice = frappe.db.get_value(reference_type, reference_name,
 					["docstatus", "outstanding_amount"], as_dict=1)
 
diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 92803a6..ea76126 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -535,6 +535,20 @@
 			"amount": self.total_allocated_amount * (tax_details['tax']['rate'] / 100)
 		}
 
+	def set_gain_or_loss(self, account_details=None):
+		if not self.difference_amount:
+			self.set_difference_amount()
+
+		row = {
+			'amount': self.difference_amount
+		}
+
+		if account_details:
+			row.update(account_details)
+
+		self.append('deductions', row)
+		self.set_unallocated_amount()
+
 @frappe.whitelist()
 def get_outstanding_reference_documents(args):
 
diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js
index 4c24a9f..df31cde 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js
@@ -16,6 +16,20 @@
 			})[0].outstanding_amount;
 
 			frappe.model.set_value(cdt, cdn, "allocated_amount", Math.min(invoice_amount, row.amount));
+
+			frm.call({
+				doc: frm.doc,
+				method: 'get_difference_amount',
+				args: {
+					child_row: row
+				},
+				callback: function(r, rt) {
+					if(r.message) {
+						frappe.model.set_value(cdt, cdn,
+							"difference_amount", r.message);
+					}
+				}
+			});
 		}
 	}
 });
@@ -104,6 +118,91 @@
 
 	reconcile: function() {
 		var me = this;
+		var show_dialog = me.frm.doc.payments.filter(d => d.difference_amount && !d.difference_account);
+
+		if (show_dialog && show_dialog.length) {
+
+			this.data = [];
+			const dialog = new frappe.ui.Dialog({
+				title: __("Select Difference Account"),
+				fields: [
+					{
+						fieldname: "payments", fieldtype: "Table", label: __("Payments"),
+						data: this.data, in_place_edit: true,
+						get_data: () => {
+							return this.data;
+						},
+						fields: [{
+							fieldtype:'Data',
+							fieldname:"docname",
+							in_list_view: 1,
+							hidden: 1
+						}, {
+							fieldtype:'Data',
+							fieldname:"reference_name",
+							label: __("Voucher No"),
+							in_list_view: 1,
+							read_only: 1
+						}, {
+							fieldtype:'Link',
+							options: 'Account',
+							in_list_view: 1,
+							label: __("Difference Account"),
+							fieldname: 'difference_account',
+							reqd: 1,
+							get_query: function() {
+								return {
+									filters: {
+										company: me.frm.doc.company,
+										is_group: 0
+									}
+								}
+							}
+						}, {
+							fieldtype:'Currency',
+							in_list_view: 1,
+							label: __("Difference Amount"),
+							fieldname: 'difference_amount',
+							read_only: 1
+						}]
+					},
+				],
+				primary_action: function() {
+					const args = dialog.get_values()["payments"];
+
+					args.forEach(d => {
+						frappe.model.set_value("Payment Reconciliation Payment", d.docname,
+							"difference_account", d.difference_account);
+					})
+
+					me.reconcile_payment_entries();
+					dialog.hide();
+				},
+				primary_action_label: __('Reconcile Entries')
+			});
+
+			this.frm.doc.payments.forEach(d => {
+				if (d.difference_amount && !d.difference_account) {
+					dialog.fields_dict.payments.df.data.push({
+						'docname': d.name,
+						'reference_name': d.reference_name,
+						'difference_amount': d.difference_amount,
+						'difference_account': d.difference_account,
+					});
+				}
+			});
+
+			this.data = dialog.fields_dict.payments.df.data;
+			dialog.fields_dict.payments.grid.refresh();
+			dialog.show();
+		} else {
+			this.reconcile_payment_entries();
+		}
+	},
+
+	reconcile_payment_entries: function() {
+		var me = this;
+
 		return this.frm.call({
 			doc: me.frm.doc,
 			method: 'reconcile',
diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index a625494..b74eed5 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -3,10 +3,11 @@
 
 from __future__ import unicode_literals
 import frappe, erpnext
-from frappe.utils import flt
+from frappe.utils import flt, today
 from frappe import msgprint, _
 from frappe.model.document import Document
-from erpnext.accounts.utils import get_outstanding_invoices
+from erpnext.accounts.utils import (get_outstanding_invoices,
+	update_reference_in_payment_entry, reconcile_against_document)
 from erpnext.controllers.accounts_controller import get_advance_payment_entries
 
 class PaymentReconciliation(Document):
@@ -20,7 +21,10 @@
 		payment_entries = self.get_payment_entries()
 		journal_entries = self.get_jv_entries()
 
-		self.add_payment_entries(payment_entries + journal_entries)
+		if self.party_type in ["Customer", "Supplier"]:
+			dr_or_cr_notes = self.get_dr_or_cr_notes()
+
+		self.add_payment_entries(payment_entries + journal_entries + dr_or_cr_notes)
 
 	def get_payment_entries(self):
 		order_doctype = "Sales Order" if self.party_type=="Customer" else "Purchase Order"
@@ -71,6 +75,34 @@
 
 		return list(journal_entries)
 
+	def get_dr_or_cr_notes(self):
+		dr_or_cr = ("credit_in_account_currency"
+			if erpnext.get_party_account_type(self.party_type) == 'Receivable' else "debit_in_account_currency")
+
+		reconciled_dr_or_cr =  ("debit_in_account_currency"
+			if dr_or_cr == "credit_in_account_currency" else "credit_in_account_currency")
+
+		voucher_type = ('Sales Invoice'
+			if self.party_type == 'Customer' else "Purchase Invoice")
+
+		return frappe.db.sql(""" SELECT `tab{doc}`.name as reference_name, %(voucher_type)s as reference_type,
+				(sum(`tabGL Entry`.{dr_or_cr}) - sum(`tabGL Entry`.{reconciled_dr_or_cr})) as amount
+			FROM `tab{doc}`, `tabGL Entry`
+			WHERE
+				(`tab{doc}`.name = `tabGL Entry`.against_voucher or `tab{doc}`.name = `tabGL Entry`.voucher_no)
+				and `tab{doc}`.is_return = 1 and `tabGL Entry`.against_voucher_type = %(voucher_type)s
+				and `tab{doc}`.docstatus = 1 and `tabGL Entry`.party = %(party)s
+				and `tabGL Entry`.party_type = %(party_type)s and `tabGL Entry`.account = %(account)s
+			GROUP BY `tabSales Invoice`.name
+			Having
+				amount > 0
+		""".format(doc=voucher_type, dr_or_cr=dr_or_cr, reconciled_dr_or_cr=reconciled_dr_or_cr), {
+			'party': self.party,
+			'party_type': self.party_type,
+			'voucher_type': voucher_type,
+			'account': self.receivable_payable_account
+		}, as_dict=1)
+
 	def add_payment_entries(self, entries):
 		self.set('payments', [])
 		for e in entries:
@@ -114,36 +146,67 @@
 			if erpnext.get_party_account_type(self.party_type) == 'Receivable' else "debit_in_account_currency")
 
 		lst = []
+		dr_or_cr_notes = []
 		for e in self.get('payments'):
+			reconciled_entry = []
 			if e.invoice_number and e.allocated_amount:
-				lst.append(frappe._dict({
-					'voucher_type': e.reference_type,
-					'voucher_no' : e.reference_name,
-					'voucher_detail_no' : e.reference_row,
-					'against_voucher_type' : e.invoice_type,
-					'against_voucher'  : e.invoice_number,
-					'account' : self.receivable_payable_account,
-					'party_type': self.party_type,
-					'party': self.party,
-					'is_advance' : e.is_advance,
-					'dr_or_cr' : dr_or_cr,
-					'unadjusted_amount' : flt(e.amount),
-					'allocated_amount' : flt(e.allocated_amount)
-				}))
+				if e.reference_type in ['Sales Invoice', 'Purchase Invoice']:
+					reconciled_entry = dr_or_cr_notes
+				else:
+					reconciled_entry = lst
+
+				reconciled_entry.append(self.get_payment_details(e, dr_or_cr))
 
 		if lst:
-			from erpnext.accounts.utils import reconcile_against_document
 			reconcile_against_document(lst)
 
-			msgprint(_("Successfully Reconciled"))
-			self.get_unreconciled_entries()
+		if dr_or_cr_notes:
+			reconcile_dr_cr_note(dr_or_cr_notes)
+
+		msgprint(_("Successfully Reconciled"))
+		self.get_unreconciled_entries()
+
+	def get_payment_details(self, row, dr_or_cr):
+		return frappe._dict({
+			'voucher_type': row.reference_type,
+			'voucher_no' : row.reference_name,
+			'voucher_detail_no' : row.reference_row,
+			'against_voucher_type' : row.invoice_type,
+			'against_voucher'  : row.invoice_number,
+			'account' : self.receivable_payable_account,
+			'party_type': self.party_type,
+			'party': self.party,
+			'is_advance' : row.is_advance,
+			'dr_or_cr' : dr_or_cr,
+			'unadjusted_amount' : flt(row.amount),
+			'allocated_amount' : flt(row.allocated_amount),
+			'difference_amount': row.difference_amount,
+			'difference_account': row.difference_account
+		})
+
+	def get_difference_amount(self, child_row):
+		if child_row.get("reference_type") != 'Payment Entry': return
+
+		child_row = frappe._dict(child_row)
+
+		if child_row.invoice_number and " | " in child_row.invoice_number:
+			child_row.invoice_type, child_row.invoice_number = child_row.invoice_number.split(" | ")
+
+		dr_or_cr = ("credit_in_account_currency"
+			if erpnext.get_party_account_type(self.party_type) == 'Receivable' else "debit_in_account_currency")
+
+		row = self.get_payment_details(child_row, dr_or_cr)
+
+		doc = frappe.get_doc(row.voucher_type, row.voucher_no)
+		update_reference_in_payment_entry(row, doc, do_not_save=True)
+
+		return doc.difference_amount
 
 	def check_mandatory_to_fetch(self):
 		for fieldname in ["company", "party_type", "party", "receivable_payable_account"]:
 			if not self.get(fieldname):
 				frappe.throw(_("Please select {0} first").format(self.meta.get_label(fieldname)))
 
-
 	def validate_invoice(self):
 		if not self.get("invoices"):
 			frappe.throw(_("No records found in the Invoice table"))
@@ -188,3 +251,41 @@
 			cond += " and `{0}` <= {1}".format(dr_or_cr, flt(self.maximum_amount))
 
 		return cond
+
+def reconcile_dr_cr_note(dr_cr_notes):
+	for d in dr_cr_notes:
+		voucher_type = ('Credit Note'
+			if d.voucher_type == 'Sales Invoice' else 'Debit Note')
+
+		dr_or_cr = ('credit_in_account_currency'
+			if d.reference_type == 'Sales Invoice' else 'debit_in_account_currency')
+
+		reconcile_dr_or_cr = ('debit_in_account_currency'
+			if dr_or_cr == 'credit_in_account_currency' else 'credit_in_account_currency')
+
+		jv = frappe.get_doc({
+			"doctype": "Journal Entry",
+			"voucher_type": voucher_type,
+			"posting_date": today(),
+			"accounts": [
+				{
+					'account': d.account,
+					'party': d.party,
+					'party_type': d.party_type,
+					reconcile_dr_or_cr: (abs(d.allocated_amount)
+						if abs(d.unadjusted_amount) > abs(d.allocated_amount) else abs(d.unadjusted_amount)),
+					'reference_type': d.against_voucher_type,
+					'reference_name': d.against_voucher
+				},
+				{
+					'account': d.account,
+					'party': d.party,
+					'party_type': d.party_type,
+					dr_or_cr: abs(d.allocated_amount),
+					'reference_type': d.voucher_type,
+					'reference_name': d.voucher_no
+				}
+			]
+		})
+
+		jv.submit()
\ No newline at end of file
diff --git a/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json b/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json
index 814257c..018bfd0 100644
--- a/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json
+++ b/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json
@@ -1,389 +1,127 @@
 {
- "allow_copy": 0, 
- "allow_events_in_timeline": 0, 
- "allow_guest_to_view": 0, 
- "allow_import": 0, 
- "allow_rename": 0, 
- "beta": 0, 
- "creation": "2014-07-09 16:13:35.452759", 
- "custom": 0, 
- "docstatus": 0, 
- "doctype": "DocType", 
- "document_type": "", 
- "editable_grid": 1, 
+ "creation": "2014-07-09 16:13:35.452759",
+ "doctype": "DocType",
+ "editable_grid": 1,
+ "field_order": [
+  "reference_type",
+  "reference_name",
+  "posting_date",
+  "is_advance",
+  "reference_row",
+  "col_break1",
+  "invoice_number",
+  "amount",
+  "allocated_amount",
+  "section_break_10",
+  "difference_account",
+  "difference_amount",
+  "sec_break1",
+  "remark"
+ ],
  "fields": [
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "reference_type", 
-   "fieldtype": "Link", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 0, 
-   "in_standard_filter": 0, 
-   "label": "Reference Type", 
-   "length": 0, 
-   "no_copy": 0, 
-   "options": "DocType", 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "fieldname": "reference_type",
+   "fieldtype": "Link",
+   "label": "Reference Type",
+   "options": "DocType",
+   "read_only": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 3, 
-   "fieldname": "reference_name", 
-   "fieldtype": "Dynamic Link", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 1, 
-   "in_standard_filter": 0, 
-   "label": "Reference Name", 
-   "length": 0, 
-   "no_copy": 0, 
-   "options": "reference_type", 
-   "permlevel": 0, 
-   "precision": "", 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "columns": 2,
+   "fieldname": "reference_name",
+   "fieldtype": "Dynamic Link",
+   "in_list_view": 1,
+   "label": "Reference Name",
+   "options": "reference_type",
+   "read_only": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "posting_date", 
-   "fieldtype": "Date", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 0, 
-   "in_standard_filter": 0, 
-   "label": "Posting Date", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "fieldname": "posting_date",
+   "fieldtype": "Date",
+   "label": "Posting Date",
+   "read_only": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "is_advance", 
-   "fieldtype": "Data", 
-   "hidden": 1, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 0, 
-   "in_standard_filter": 0, 
-   "label": "Is Advance", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "fieldname": "is_advance",
+   "fieldtype": "Data",
+   "hidden": 1,
+   "label": "Is Advance",
+   "read_only": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "reference_row", 
-   "fieldtype": "Data", 
-   "hidden": 1, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 0, 
-   "in_standard_filter": 0, 
-   "label": "Reference Row", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "fieldname": "reference_row",
+   "fieldtype": "Data",
+   "hidden": 1,
+   "label": "Reference Row",
+   "read_only": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "col_break1", 
-   "fieldtype": "Column Break", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 0, 
-   "in_standard_filter": 0, 
-   "label": "", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 0, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "fieldname": "col_break1",
+   "fieldtype": "Column Break"
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 3, 
-   "fieldname": "invoice_number", 
-   "fieldtype": "Select", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 1, 
-   "in_standard_filter": 0, 
-   "label": "Invoice Number", 
-   "length": 0, 
-   "no_copy": 0, 
-   "options": "", 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 0, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 1, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "columns": 2,
+   "fieldname": "invoice_number",
+   "fieldtype": "Select",
+   "in_list_view": 1,
+   "label": "Invoice Number",
+   "reqd": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 2, 
-   "fieldname": "amount", 
-   "fieldtype": "Currency", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 1, 
-   "in_standard_filter": 0, 
-   "label": "Amount", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "columns": 2,
+   "fieldname": "amount",
+   "fieldtype": "Currency",
+   "in_list_view": 1,
+   "label": "Amount",
+   "read_only": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 2, 
-   "fieldname": "allocated_amount", 
-   "fieldtype": "Currency", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 1, 
-   "in_standard_filter": 0, 
-   "label": "Allocated amount", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "precision": "", 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 0, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 1, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "columns": 2,
+   "fieldname": "allocated_amount",
+   "fieldtype": "Currency",
+   "in_list_view": 1,
+   "label": "Allocated amount",
+   "reqd": 1
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "sec_break1", 
-   "fieldtype": "Section Break", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 0, 
-   "in_standard_filter": 0, 
-   "label": "", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 0, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
-  }, 
+   "fieldname": "sec_break1",
+   "fieldtype": "Section Break"
+  },
   {
-   "allow_bulk_edit": 0, 
-   "allow_in_quick_entry": 0, 
-   "allow_on_submit": 0, 
-   "bold": 0, 
-   "collapsible": 0, 
-   "columns": 0, 
-   "fieldname": "remark", 
-   "fieldtype": "Small Text", 
-   "hidden": 0, 
-   "ignore_user_permissions": 0, 
-   "ignore_xss_filter": 0, 
-   "in_filter": 0, 
-   "in_global_search": 0, 
-   "in_list_view": 1, 
-   "in_standard_filter": 0, 
-   "label": "Remark", 
-   "length": 0, 
-   "no_copy": 0, 
-   "permlevel": 0, 
-   "print_hide": 0, 
-   "print_hide_if_no_value": 0, 
-   "read_only": 1, 
-   "remember_last_selected_value": 0, 
-   "report_hide": 0, 
-   "reqd": 0, 
-   "search_index": 0, 
-   "set_only_once": 0, 
-   "translatable": 0, 
-   "unique": 0
+   "fieldname": "remark",
+   "fieldtype": "Small Text",
+   "in_list_view": 1,
+   "label": "Remark",
+   "read_only": 1
+  },
+  {
+   "columns": 2,
+   "fieldname": "difference_account",
+   "fieldtype": "Link",
+   "in_list_view": 1,
+   "label": "Difference Account",
+   "options": "Account"
+  },
+  {
+   "fieldname": "difference_amount",
+   "fieldtype": "Currency",
+   "label": "Difference Amount",
+   "print_hide": 1,
+   "read_only": 1
+  },
+  {
+   "fieldname": "section_break_10",
+   "fieldtype": "Section Break"
   }
- ], 
- "has_web_view": 0, 
- "hide_heading": 0, 
- "hide_toolbar": 0, 
- "idx": 0, 
- "image_view": 0, 
- "in_create": 0, 
- "is_submittable": 0, 
- "issingle": 0, 
- "istable": 1, 
- "max_attachments": 0, 
- "menu_index": 0, 
- "modified": "2019-01-07 16:52:07.567027", 
- "modified_by": "Administrator", 
- "module": "Accounts", 
- "name": "Payment Reconciliation Payment", 
- "name_case": "", 
- "owner": "Administrator", 
- "permissions": [], 
- "quick_entry": 1, 
- "read_only": 0, 
- "read_only_onload": 0, 
- "show_name_in_global_search": 0, 
- "sort_field": "modified", 
- "sort_order": "DESC", 
- "track_changes": 0, 
- "track_seen": 0, 
- "track_views": 0
+ ],
+ "istable": 1,
+ "modified": "2019-06-24 00:08:11.150796",
+ "modified_by": "Administrator",
+ "module": "Accounts",
+ "name": "Payment Reconciliation Payment",
+ "owner": "Administrator",
+ "permissions": [],
+ "quick_entry": 1,
+ "sort_field": "modified",
+ "sort_order": "DESC"
 }
\ No newline at end of file
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 7a230a7..7a1f6c5 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -435,7 +435,7 @@
 	jv_obj.flags.ignore_validate_update_after_submit = True
 	jv_obj.save(ignore_permissions=True)
 
-def update_reference_in_payment_entry(d, payment_entry):
+def update_reference_in_payment_entry(d, payment_entry, do_not_save=False):
 	reference_details = {
 		"reference_doctype": d.against_voucher_type,
 		"reference_name": d.against_voucher,
@@ -466,7 +466,17 @@
 	payment_entry.setup_party_account_field()
 	payment_entry.set_missing_values()
 	payment_entry.set_amounts()
-	payment_entry.save(ignore_permissions=True)
+
+	if d.difference_amount and d.difference_account:
+		payment_entry.set_gain_or_loss(account_details={
+			'account': d.difference_account,
+			'cost_center': payment_entry.cost_center or frappe.get_cached_value('Company',
+				payment_entry.company, "cost_center"),
+			'amount': d.difference_amount
+		})
+
+	if not do_not_save:
+		payment_entry.save(ignore_permissions=True)
 
 def unlink_ref_doc_from_payment_entries(ref_doc):
 	remove_ref_doc_link_from_jv(ref_doc.doctype, ref_doc.name)