GST compliance is the mandatory practice. The maximum amount in distributors in 2024 was Rs.10,000 imposed on a Pune-based mid-size distributor because they forgot to file the GST-3B within 2 days of the date they were supposed to do so. Their accounts department presupposed an extension of the public holidays. It didn’t. The lesson? GST penalties are not necessarily related to fraud, and they may be associated with gaps in memory or incorrect invoice number formats or uncontrolled E-Way Bills. These small omissions can grow out of proportion into costly compliance headaches as the financial year ends.
When you are a sales head like Priya and have to report to various invoices and clients, here is your checklist of GST Compliance quicker because it is always cheaper than cure.

⚠️ GST Penalties: Quick Breakdown.
And then before exploring in details the Compliance Checklist, we need to decipher the most important penalties that most MSMEs fall prey to:
- Late GSTR 3B Filing: ₹50 per day (₹25 CGST + ₹25 SGST) for returns with tax liability. Nil returns? ₹20 per day.
- → In case of Nil return if return maximum penalty amount is ₹500 — easy to miss, harder to reverse.
- Wrong E-Invoicing Format: ₹10,000 per incorrect invoice (or 100% of the tax due, whichever is higher). Adhering to the format is key to your GST Tax Filing.
- E-Way Bill Errors: ₹10,000 penalty or tax equivalent on goods transported without valid documentation.
- Mismatch between GSTR-1 and GSTR 3B: Triggers scrutiny notices and ITC disallowance.
- Delayed Payment of GST: 18% per annum interest till the date of payment.
These are not imaginary, they are real-life situations that small businesses have to deal with on a quarterly basis.
✅ Your 5-Point GST Compliance Checklist (Actionable & Year-End Ready)
This Checklist will be very helpful in helping you prepare your year end.
1️⃣ Rule 48 Compliance E-Invoicing Review.
- Confirm whether your turnover passed Rs. 5 crore mark- now compulsory.
- Make sure that all invoices are issued by IRP (Invoice Registration Portal).
- crying Keep invoice format updated with Gstin codes,hallSBIN of supplier and recipient.
💡 Bonus tip: You want to ensure that you do not have any dangerous E-invoices on your records? Connect your ERP or billing software to E-invoicing APIs.
2️⃣ GSTR-3B Filing Discipline
- Indicate your filing calendar of GST returns – no presumptions of due date relaxation.
- Even NIL files are returned on time to prevent penalties of daily GST.
- Match external supplies (GSTR-1) to GSTR-3B on a monthly basis as a way of identifying an early-warning.
📅 Nuance: There is an accrual of the penalty on Section 47(1). Missed GST return Filing also postpones ITC to your purchasers – this is a factor of your business integrity.
3️⃣ E-Way Bill Validation
- Create E-Way Bills prior to dispatch – do not back date or use hand slips.
- Compare E-Way Bill information and invoice facts.
- Check the transporter and vehicle details are updated – out of date validity = may be seized.
🧾 Hack: E-Way Bill creation should be automated and associated with the sales dispatch systems. It is an imperative move in your current Checklist.
4️⃣ GST Reconciliation of payments and ITC.
- The existence of ITC claimed, which is against GSTR-2B, should be checked.
- Remit arrears of GST before the due date to save 18 per cent interest.
- Vendor GST Filing patterns Track a non-compliant vendor and stop your ITC.
🔍 Compliance Decoder Tip: Accuracy on monthly basis: AI-based reconciliation tools (we can assist in deploying this) are used.
5️⃣ Record Retention & Annual Return Prep (GSTR-9).
- Retain invoice and challan information of 6 years.
- Begin preparation of GSTR-9 early enough – not in December.
- ITC, turnover and tax liability summaries.
📦 Insight: The frequent cause of show-cause notices when auditing is the lack of backup data. An effective GST Compliance Checklist involves a good record keeping.
💬 Summary -Keep in Line, Keep in Confidence.
GST is not supposed to punish, it is intended to discipline. The most intelligent businesses are the ones that do not always go right, but those ones that identify the mistakes early with the help of a strong GST Compliance Checklist. We work with MSMEs at Accdig to automate compliance because E-Invoicing, GST return Filing, or AI-based reconciliations are only a few of the many ways to use compliance to make sales, and not Penalties.
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