diff --git a/erpnext/accounts/report/gross_profit/gross_profit.py b/erpnext/accounts/report/gross_profit/gross_profit.py
index fde4de8402..01fee281b0 100644
--- a/erpnext/accounts/report/gross_profit/gross_profit.py
+++ b/erpnext/accounts/report/gross_profit/gross_profit.py
@@ -501,7 +501,14 @@ class GrossProfitGenerator(object):
 						):
 							returned_item_rows = self.returned_invoices[row.parent][row.item_code]
 							for returned_item_row in returned_item_rows:
-								row.qty += flt(returned_item_row.qty)
+								# returned_items 'qty' should be stateful
+								if returned_item_row.qty != 0:
+									if row.qty >= abs(returned_item_row.qty):
+										row.qty += returned_item_row.qty
+										returned_item_row.qty = 0
+									else:
+										row.qty = 0
+										returned_item_row.qty += row.qty
 								row.base_amount += flt(returned_item_row.base_amount, self.currency_precision)
 							row.buying_amount = flt(flt(row.qty) * flt(row.buying_rate), self.currency_precision)
 						if flt(row.qty) or row.base_amount:
@@ -734,6 +741,8 @@ class GrossProfitGenerator(object):
 		if self.filters.to_date:
 			conditions += " and posting_date <= %(to_date)s"
 
+		conditions += " and (is_return = 0 or (is_return=1 and return_against is null))"
+
 		if self.filters.item_group:
 			conditions += " and {0}".format(get_item_group_condition(self.filters.item_group))
 
diff --git a/erpnext/accounts/report/gross_profit/test_gross_profit.py b/erpnext/accounts/report/gross_profit/test_gross_profit.py
index 21681bef5b..82fe1a0ba1 100644
--- a/erpnext/accounts/report/gross_profit/test_gross_profit.py
+++ b/erpnext/accounts/report/gross_profit/test_gross_profit.py
@@ -381,3 +381,82 @@ class TestGrossProfit(FrappeTestCase):
 		}
 		gp_entry = [x for x in data if x.parent_invoice == sinv.name]
 		self.assertDictContainsSubset(expected_entry, gp_entry[0])
+
+	def test_crnote_against_invoice_with_multiple_instances_of_same_item(self):
+		"""
+		Item Qty for Sales Invoices with multiple instances of same item go in the -ve. Ideally, the credit noteshould cancel out the invoice items.
+		"""
+		from erpnext.accounts.doctype.sales_invoice.sales_invoice import make_sales_return
+
+		# Invoice with an item added twice
+		sinv = self.create_sales_invoice(qty=1, rate=100, posting_date=nowdate(), do_not_submit=True)
+		sinv.append("items", frappe.copy_doc(sinv.items[0], ignore_no_copy=False))
+		sinv = sinv.save().submit()
+
+		# Create Credit Note for Invoice
+		cr_note = make_sales_return(sinv.name)
+		cr_note = cr_note.save().submit()
+
+		filters = frappe._dict(
+			company=self.company, from_date=nowdate(), to_date=nowdate(), group_by="Invoice"
+		)
+
+		columns, data = execute(filters=filters)
+		expected_entry = {
+			"parent_invoice": sinv.name,
+			"currency": "INR",
+			"sales_invoice": self.item,
+			"customer": self.customer,
+			"posting_date": frappe.utils.datetime.date.fromisoformat(nowdate()),
+			"item_code": self.item,
+			"item_name": self.item,
+			"warehouse": "Stores - _GP",
+			"qty": 0.0,
+			"avg._selling_rate": 0.0,
+			"valuation_rate": 0.0,
+			"selling_amount": -100.0,
+			"buying_amount": 0.0,
+			"gross_profit": -100.0,
+			"gross_profit_%": 100.0,
+		}
+		gp_entry = [x for x in data if x.parent_invoice == sinv.name]
+		# Both items of Invoice should have '0' qty
+		self.assertEqual(len(gp_entry), 2)
+		self.assertDictContainsSubset(expected_entry, gp_entry[0])
+		self.assertDictContainsSubset(expected_entry, gp_entry[1])
+
+	def test_standalone_cr_notes(self):
+		"""
+		Standalone cr notes will be reported as usual
+		"""
+		# Make Cr Note
+		sinv = self.create_sales_invoice(
+			qty=-1, rate=100, posting_date=nowdate(), do_not_save=True, do_not_submit=True
+		)
+		sinv.is_return = 1
+		sinv = sinv.save().submit()
+
+		filters = frappe._dict(
+			company=self.company, from_date=nowdate(), to_date=nowdate(), group_by="Invoice"
+		)
+
+		columns, data = execute(filters=filters)
+		expected_entry = {
+			"parent_invoice": sinv.name,
+			"currency": "INR",
+			"sales_invoice": self.item,
+			"customer": self.customer,
+			"posting_date": frappe.utils.datetime.date.fromisoformat(nowdate()),
+			"item_code": self.item,
+			"item_name": self.item,
+			"warehouse": "Stores - _GP",
+			"qty": -1.0,
+			"avg._selling_rate": 100.0,
+			"valuation_rate": 0.0,
+			"selling_amount": -100.0,
+			"buying_amount": 0.0,
+			"gross_profit": -100.0,
+			"gross_profit_%": 100.0,
+		}
+		gp_entry = [x for x in data if x.parent_invoice == sinv.name]
+		self.assertDictContainsSubset(expected_entry, gp_entry[0])