diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index 5b6e7066743..257434fb895 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -180,7 +180,7 @@ class StockReconciliation(StockController):
 				frappe.throw(_("Valuation Rate required for Item in row {0}").format(row.idx))
 
 			if ((previous_sle and row.qty == previous_sle.get("qty_after_transaction")
-				and row.valuation_rate == previous_sle.get("valuation_rate"))
+				and (row.valuation_rate == previous_sle.get("valuation_rate") or row.qty == 0))
 				or (not previous_sle and not row.qty)):
 					continue
 
diff --git a/erpnext/stock/stock_ledger.py b/erpnext/stock/stock_ledger.py
index 43140faff6b..c73cbf29421 100644
--- a/erpnext/stock/stock_ledger.py
+++ b/erpnext/stock/stock_ledger.py
@@ -176,7 +176,7 @@ class update_entries_after(object):
 		# rounding as per precision
 		self.stock_value = flt(self.stock_value, self.precision)
 
-		if self.prev_stock_value < 0 and self.stock_value >= 0:
+		if self.prev_stock_value < 0 and self.stock_value >= 0 and sle.voucher_type != 'Stock Reconciliation':
 			stock_value_difference = sle.actual_qty * self.valuation_rate
 		else:
 			stock_value_difference = self.stock_value - self.prev_stock_value