Make a vendor for Bank, define GSTIN of Bank on this vendor.
Make a separate posting profile "Bank charges" and attach GL "Bank Charges Control GL".
While receiving the bank charges in the bank statement on daily basis, keep it book with entry:
Vendor (Bank) Dr. to Bank
It will book the entries of "Bank charges control GL" debit and bank credit.
It will serve the purpose of Bank reconciliation since bank entries are happening.
At month-end, once we receive the Invoice of bank charges from Bank, book it similar to other expenses.
Bank charges GL Dr. to Vendor (Bank) with consolidated amount.
It will help to track the bank charges in control GL and reconcile with invoice at month-end. Benefits of this solution:
1) It will reflect in GSTR-2 report as input.
2) Reconciliation of bank charges on daily basis.
3) Reconciliation of bank charges invoice at month-end.
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