diff --git a/packages/material-react-table/src/components/inputs/MRT_SelectCheckbox.tsx b/packages/material-react-table/src/components/inputs/MRT_SelectCheckbox.tsx
index 03c3f53d6..346c14673 100644
--- a/packages/material-react-table/src/components/inputs/MRT_SelectCheckbox.tsx
+++ b/packages/material-react-table/src/components/inputs/MRT_SelectCheckbox.tsx
@@ -43,10 +43,15 @@ export const MRT_SelectCheckbox = <TData extends MRT_RowData>({
 
   const selectAll = !row;
 
+  const getLeafRows = () => (
+    selectAllMode === 'page'
+    ? table.getPaginationRowModel().flatRows
+    : table.getPrePaginationRowModel().flatRows
+  ).filter((r) => !r.getIsGrouped());
+
+  // Fix: getIsAllPageRowsSelected() / getIsAllRowsSelected() include group rows
   const allRowsSelected = selectAll
-    ? selectAllMode === 'page'
-      ? table.getIsAllPageRowsSelected()
-      : table.getIsAllRowsSelected()
+    ? getLeafRows().every((r) => r.getIsSelected())
     : undefined;
 
   const isChecked = selectAll
@@ -122,7 +127,8 @@ export const MRT_SelectCheckbox = <TData extends MRT_RowData>({
         <Checkbox
           indeterminate={
             !isChecked && selectAll
-              ? table.getIsSomeRowsSelected()
+              ? // Fix: getIsSomeRowsSelected() includes group rows, use leaf-only filter
+                getLeafRows().some((r) => r.getIsSelected())
               : row?.getIsSomeSelected() && row.getCanSelectSubRows()
           }
           {...commonProps}
diff --git a/packages/material-react-table/src/utils/row.utils.ts b/packages/material-react-table/src/utils/row.utils.ts
index 576bc0060..bc17dddea 100644
--- a/packages/material-react-table/src/utils/row.utils.ts
+++ b/packages/material-react-table/src/utils/row.utils.ts
@@ -175,6 +175,16 @@ export const getMRT_RowSelectionHandler =
 
     const wasCurrentRowChecked = getIsRowSelected({ row, table });
 
+    // Fix: toggleSelected() on a group row also writes its own ID into rowSelection 
+    // Removing it, keeping only the leaf row IDs
+    if (row.getIsGrouped()) {
+      table.setRowSelection((prev) => {
+        const next = { ...prev };
+        delete next[row.id];
+        return next;
+      });
+    }
+
     // toggle selection of this row
     row.toggleSelected(value ?? !wasCurrentRowChecked);
 
@@ -250,9 +260,17 @@ export const getMRT_SelectAllHandler =
       refs: { lastSelectedRowId },
     } = table;
 
-    selectAllMode === 'all' || forceAll
-      ? table.toggleAllRowsSelected(value ?? (event as any).target.checked)
-      : table.toggleAllPageRowsSelected(value ?? (event as any).target.checked);
+    // Fix: replaces toggleAllPageRowsSelected() / toggleAllRowsSelected() which
+    // include group rows in flatRows, causing group IDs to pollute rowSelection.
+    const checked = value ?? (event as any).target.checked;
+    const rows = (selectAllMode === 'all' || forceAll
+      ? table.getPrePaginationRowModel().flatRows
+      : table.getPaginationRowModel().flatRows
+    ).filter((row) => !row.getIsGrouped());
+    rows.forEach((row) => {
+      if (row.getCanSelect()) row.toggleSelected(checked);
+    });
+    
     if (enableRowPinning && rowPinningDisplayMode?.includes('select')) {
       table.setRowPinning({ bottom: [], top: [] });
     }