diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.js b/erpnext/accounts/doctype/payment_entry/payment_entry.js
index 776bacf..fc3eed3 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.js
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.js
@@ -588,6 +588,10 @@
 	allocate_party_amount_against_ref_docs: function(frm, paid_amount) {
 		var total_positive_outstanding_including_order = 0;
 		var total_negative_outstanding = 0;
+		var total_deductions = frappe.utils.sum($.map(frm.doc.deductions || [],
+			function(d) { return flt(d.amount) }));
+
+		paid_amount -= total_deductions;
 
 		$.each(frm.doc.references || [], function(i, row) {
 			if(flt(row.outstanding_amount) > 0)
diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 2f8e6b8..4e99859 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -337,14 +337,15 @@
 			total_negative_outstanding = sum([abs(flt(d.outstanding_amount))
 				for d in self.get("references") if flt(d.outstanding_amount) < 0])
 
-			party_amount = self.paid_amount if self.payment_type=="Receive" else self.received_amount
+			paid_amount = self.paid_amount if self.payment_type=="Receive" else self.received_amount
+			additional_charges = sum([flt(d.amount) for d in self.deductions])
 
 			if not total_negative_outstanding:
 				frappe.throw(_("Cannot {0} {1} {2} without any negative outstanding invoice")
 					.format(self.payment_type, ("to" if self.party_type=="Customer" else "from"),
 						self.party_type), InvalidPaymentEntry)
 
-			elif party_amount > total_negative_outstanding:
+			elif paid_amount - additional_charges > total_negative_outstanding:
 				frappe.throw(_("Paid Amount cannot be greater than total negative outstanding amount {0}")
 					.format(total_negative_outstanding), InvalidPaymentEntry)