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Bookkeeping mistakes that cause GST/IT notices

Most GST and income tax notices for small businesses come from mismatches the department can see in its own data: input tax credit not matching GSTR-2B, sales in GST returns not matching the ITR, cash deposits without records, or TDS not reflected. Monthly bookkeeping with bank and GST reconciliation prevents most of them.

By Saurabh AgrawalReviewed by SkyGTax in-house CA teamUpdated {{ updated }}3 min read

Mistakes that commonly lead to notices

1. Claiming ITC not in GSTR-2B

Input tax credit claimed beyond what suppliers have reported shows up immediately. It can lead to reversal, interest and a notice.

2. GST turnover not matching the ITR

The department compares turnover in GST returns with the income tax return. Differences from credit notes, advances or timing must be explainable from your books.

3. Unrecorded cash sales

Cash deposited in the bank but missing from the books looks like unexplained income. Record cash sales daily.

4. Mixing personal and business transactions

Personal spending in business accounts distorts profit and makes scrutiny harder to answer.

5. TDS not deducted or not matched

Missing TDS on rent, contractor or professional payments can disallow the expense. TDS deducted by customers that you do not record creates mismatches with Form 26AS.

6. No stock records

Without stock records, it is difficult to support gross profit or answer questions on purchases that seem high.

Monthly habits that prevent notices

  1. Record every sale and purchase, including cash, in the books each month.
  2. Reconcile every bank account with the books.
  3. Match purchase entries with GSTR-2B before filing GSTR-3B.
  4. Match GSTR-1 with the sales register.
  5. Check TDS deducted by customers in Form 26AS each quarter.
  6. Keep bills and contracts for all expenses.
CheckFrequencyNotice it helps avoid
Bank reconciliationMonthlyUnexplained deposits
GSTR-2B vs purchase registerMonthlyExcess ITC
GSTR-1 vs sales registerMonthlyGSTR-1 and 3B mismatch
Form 26AS vs booksQuarterlyTDS credit mismatch
GST turnover vs ITRYearlyTurnover mismatch

Frequently asked questions

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Sources

Information is for general guidance and not a substitute for professional advice. Rules, rates and due dates change; confirm with us before acting.

More guides

ROC annual compliance checklist for companies/LLPs→UP RERA registration: who needs it and how→Income Tax Return filing guide for salaried individuals→
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