diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index 8301a706183d..674624e184b4 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -404,7 +404,9 @@ def _changed(item):
 					fields=["total_qty as qty", "avg_rate as rate"],
 				)[0]
 
+				bundle_data.qty = abs(bundle_data.qty)
 				self.calculate_difference_amount(item, bundle_data)
+
 				return True
 
 			inventory_dimensions_dict = {}
@@ -464,11 +466,16 @@ def _changed(item):
 			frappe.msgprint(_("Removed items with no change in quantity or value."))
 
 	def calculate_difference_amount(self, item, item_dict):
-		self.difference_amount += flt(item.qty, item.precision("qty")) * flt(
-			item.valuation_rate or item_dict.get("rate"), item.precision("valuation_rate")
-		) - flt(item_dict.get("qty"), item.precision("qty")) * flt(
-			item_dict.get("rate"), item.precision("valuation_rate")
-		)
+		qty_precision = item.precision("qty")
+		val_precision = item.precision("valuation_rate")
+
+		new_qty = flt(item.qty, qty_precision)
+		new_valuation_rate = flt(item.valuation_rate or item_dict.get("rate"), val_precision)
+
+		current_qty = flt(item_dict.get("qty"), qty_precision)
+		current_valuation_rate = flt(item_dict.get("rate"), val_precision)
+
+		self.difference_amount += (new_qty * new_valuation_rate) - (current_qty * current_valuation_rate)
 
 	def validate_data(self):
 		def _get_msg(row_num, msg):
diff --git a/erpnext/stock/doctype/stock_reconciliation/test_stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/test_stock_reconciliation.py
index 8845bdbb753c..a41db6cf611e 100644
--- a/erpnext/stock/doctype/stock_reconciliation/test_stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/test_stock_reconciliation.py
@@ -1109,6 +1109,7 @@ def test_not_reconcile_all_batch(self):
 		)
 
 		sr.reload()
+		self.assertEqual(sr.difference_amount, 98900.0)
 
 		self.assertTrue(sr.items[0].current_valuation_rate)
 		current_sabb = sr.items[0].current_serial_and_batch_bundle