diff --git a/erpnext/manufacturing/doctype/work_order/test_work_order.py b/erpnext/manufacturing/doctype/work_order/test_work_order.py
index e7eb9c6149..a399edda70 100644
--- a/erpnext/manufacturing/doctype/work_order/test_work_order.py
+++ b/erpnext/manufacturing/doctype/work_order/test_work_order.py
@@ -911,6 +911,54 @@ class TestWorkOrder(ERPNextTestCase):
 
 		self.assertEqual(wo1.operations[0].time_in_mins, wo2.operations[0].time_in_mins)
 
+	def test_partial_manufacture_entries(self):
+		cancel_stock_entry = []
+
+		frappe.db.set_value("Manufacturing Settings", None,
+			"backflush_raw_materials_based_on", "Material Transferred for Manufacture")
+
+		wo_order = make_wo_order_test_record(planned_start_date=now(), qty=100)
+		ste1 = test_stock_entry.make_stock_entry(item_code="_Test Item",
+			target="_Test Warehouse - _TC", qty=120, basic_rate=5000.0)
+		ste2 = test_stock_entry.make_stock_entry(item_code="_Test Item Home Desktop 100",
+			target="_Test Warehouse - _TC", qty=240, basic_rate=1000.0)
+
+		cancel_stock_entry.extend([ste1.name, ste2.name])
+
+		sm = frappe.get_doc(make_stock_entry(wo_order.name, "Material Transfer for Manufacture", 100))
+		for row in sm.get('items'):
+			if row.get('item_code') == '_Test Item':
+				row.qty = 110
+
+		sm.submit()
+		cancel_stock_entry.append(sm.name)
+
+		s = frappe.get_doc(make_stock_entry(wo_order.name, "Manufacture", 90))
+		for row in s.get('items'):
+			if row.get('item_code') == '_Test Item':
+				self.assertEqual(row.get('qty'), 100)
+		s.submit()
+		cancel_stock_entry.append(s.name)
+
+		s1 = frappe.get_doc(make_stock_entry(wo_order.name, "Manufacture", 5))
+		for row in s1.get('items'):
+			if row.get('item_code') == '_Test Item':
+				self.assertEqual(row.get('qty'), 5)
+		s1.submit()
+		cancel_stock_entry.append(s1.name)
+
+		s2 = frappe.get_doc(make_stock_entry(wo_order.name, "Manufacture", 5))
+		for row in s2.get('items'):
+			if row.get('item_code') == '_Test Item':
+				self.assertEqual(row.get('qty'), 5)
+
+		cancel_stock_entry.reverse()
+		for ste in cancel_stock_entry:
+			doc = frappe.get_doc("Stock Entry", ste)
+			doc.cancel()
+
+		frappe.db.set_value("Manufacturing Settings", None,
+			"backflush_raw_materials_based_on", "BOM")
 
 def update_job_card(job_card, jc_qty=None):
 	employee = frappe.db.get_value('Employee', {'status': 'Active'}, 'name')
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index a61b3199c0..60154afa15 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -1445,14 +1445,15 @@ class StockEntry(StockController):
 							qty = req_qty_each * flt(self.fg_completed_qty)
 
 			elif backflushed_materials.get(item.item_code):
+				precision = frappe.get_precision("Stock Entry Detail", "qty")
 				for d in backflushed_materials.get(item.item_code):
-					if d.get(item.warehouse):
+					if d.get(item.warehouse) > 0:
 						if (qty > req_qty):
-							qty = (qty/trans_qty) * flt(self.fg_completed_qty)
+							qty = ((flt(qty, precision) - flt(d.get(item.warehouse), precision))
+								/ (flt(trans_qty, precision) - flt(produced_qty, precision))
+							) * flt(self.fg_completed_qty)
 
-						if consumed_qty and frappe.db.get_single_value("Manufacturing Settings",
-							"material_consumption"):
-							qty -= consumed_qty
+							d[item.warehouse] -= qty
 
 			if cint(frappe.get_cached_value('UOM', item.stock_uom, 'must_be_whole_number')):
 				qty = frappe.utils.ceil(qty)