Rohit's GSTIN arrived last Tuesday. By the 20th of next month, he owes his first GST. Total payable: ₹18,540. He's never paid government money online before — last time he saw "challan" was on a TV news ticker.
The portal looks scary. The actual flow is six clicks.
- Login at gst.gov.in → Services → Payments → Create Challan.
- Enter the amounts under CGST / SGST / IGST / Cess heads.
- Pick a mode — Net Banking is fastest; UPI works up to ₹1L; NEFT/RTGS for very large.
- Pay, download the receipt, file it. Pay before the 18th to dodge last-day portal jams.
Payment ≠ filing — read this twice
This is where most first-timers slip. Paying GST puts money into your Electronic Cash Ledger at the GST department. It doesn't tell them what return it's for. Filing GSTR-3B is the act of declaring "here's my liability, here's how I'm clearing it from the ledger".
If you only pay and forget to file — late fees still apply. If you only file and forget to pay — interest applies. Always do both.
The 6-click flow
GSTIN as username, your password, captcha. You land on the dashboard.
Hover the top menu. Click through. New page opens.
4 columns (CGST / SGST / IGST / Cess) × 5 rows (Tax / Interest / Penalty / Fee / Other). Put numbers only in the cells that apply.
Net banking, UPI, card, NEFT/RTGS, or over-the-counter (OTC). Most users pick Net Banking or UPI.
The system issues a CPIN. You're redirected to your bank / UPI / card screen to actually pay. CPIN is valid 15 days.
The portal generates a CIN (Challan Identification Number) — your proof of payment. Save the PDF in your GST folder.
The big mistake — putting money in the wrong head
Here's where Rohit nearly tripped up. He had to pay ₹18,540 in total:
👉 Intra-state sale (within his state) — split equally: ₹9,270 CGST + ₹9,270 SGST.
👉 Inter-state sale (different state, or export) — the full ₹18,540 goes to IGST.
Putting an IGST amount under CGST/SGST means your money lands in the wrong ledger. GSTR-3B won't reconcile. You'll either need to file a PMT-09 transfer or pay again. Always check the place of supply before allocating.
Pull your GSTR-1 summary first. It tells you exactly how much went to each head this month. Use those numbers as your challan inputs. Don't guess.
Which payment mode is best?
Net Banking
The default
Fastest, free, works for any amount. Use this unless you can't.
UPI
Small-to-mid
Quick for amounts under ₹1L. Use your usual UPI app.
NEFT / RTGS
Very large amounts
Generate a mandate form, take to your bank. Useful for >₹1L.
OTC (over the counter at bank) still exists — but only for challans up to ₹10,000. Almost no one uses it. Credit/Debit card works on the e-payment screen but most cards add a 1–2% fee — skip if you can.
Three things to watch out for
👉 Challans expire in 15 days. If you create one and forget for 16 days, the CPIN is dead. Generate fresh.
👉 Pay by the 18th, not the 20th. Last-day portal slowdowns are real. Bank delays push you into interest.
👉 Save the receipt PDF. The portal copy is your only proof if a notice comes 3 years later.
The first month is a fumble. Second month takes 8 minutes. By month six, you'll be doing it during a chai break.
CPIN vs CIN — the two numbers
Both sound the same. They aren't.
👉 CPIN (Common Portal Identification Number) — generated when you create the challan. Tells the bank "this person wants to pay GST".
👉 CIN (Challan Identification Number) — generated after the bank confirms payment. This is your actual proof. Without a CIN, the money never reached the department.
If something goes wrong
👉 Payment debited but no CIN? Wait 24 hours — banks sometimes lag. Then call your bank with the UTR / reference. Also raise a ticket via Services → User Services → Grievances.
👉 Money in wrong head? File PMT-09 to transfer between heads within your Electronic Cash Ledger. Takes 1–2 days.
👉 Overpaid? Excess sits in the Cash Ledger — offset against future liabilities, or file RFD-01 for a refund. Refunds usually take 30–60 days.
Quick answers
No. Payment puts cash in your Electronic Cash Ledger. Filing GSTR-3B is the declaration of liability and the offset. You must do both — payment without filing still attracts late-filing fees of ₹50/day.
Yes — via the OTC mode, but only for challans up to ₹10,000. Above that, electronic payment is mandatory.
Money sits in your Electronic Cash Ledger. You can offset against future months, or claim refund via Form RFD-01. Refund processing usually takes 30–60 days.
CPIN = generated when challan is created (your reference to pay). CIN = generated after the bank confirms payment (your proof). CIN is what the GST department uses to recognise the payment.
Not for regular monthly GST. For arrears / demand orders, instalment requests can be filed under Section 80 of the CGST Act and require Commissioner's approval.
When you might want help
The payment flow itself is straightforward. Where founders typically get stuck: reconciling GSTR-2B input credit before deciding the cash payable amount, splitting between CGST/SGST/IGST when the customer mix is messy, and setting up a monthly checklist that pairs payment + filing so neither is forgotten.
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