Ecommerce accounting services in India.
Specialist CA-led accounting for Amazon, Flipkart, Meesho and Shopify sellers - books, GST and reconciliation handled end-to-end. Indian online sellers operate in one of the world's most compliance-heavy ecommerce tax environments. We close the books, reconcile every settlement, and file the returns so your dashboard matches the bank.
500+ sellers served · 4.8 Google rating · 50,000+ returns filed · 12+ years experience · Offices in Kolkata, Delhi, Gurugram and Pune
Reviewed by CA & CS Team · Regikart · Last updated 26 May 2026
What this service covers.
Ecommerce accounting services cover monthly bookkeeping, settlement reconciliation, GST return filing, TCS credit claim and Section 194-O TDS reconciliation for online sellers on Amazon, Flipkart, Meesho, Shopify and D2C platforms.
Regikart plans start at Rs 3,499 per month for single-platform sellers and scale with order volume.
| Parameter | Detail |
|---|---|
| Service | Bookkeeping + GST + TCS/TDS reconciliation + reporting |
| Platforms | Amazon, Flipkart, Meesho, Shopify, Myntra, WooCommerce, Nykaa |
| GST registration | Mandatory from Day 1 under Section 24(ix) CGST Act |
| TCS rate (marketplace) | 1% (0.5% CGST + 0.5% SGST) under Section 52 CGST |
| TDS u/s 194-O | 0.1% wef 1 Oct 2024 (Finance Act 2024) |
| Starting fee | Rs 3,499 per month |
| Turnaround | Monthly close in 7 working days |
Settlement is not revenue.
Ecommerce accounting is the practice of recording gross sales, marketplace deductions, returns, GST liability, TCS credits and Section 194-O TDS for online sellers operating through ecommerce operators registered under the CGST Act 2017.
Unlike traditional retail, ecommerce books must separate gross sales from net settlement, because marketplaces deduct commission, fulfilment fees, advertising charges, TCS at 1 percent and TDS at 0.1 percent before paying the seller. Recording the settlement amount as revenue is the single most common error - it overstates margin while understating GST liability.
Each marketplace publishes settlement reports in its own format - Amazon MTR, Flipkart Sales Reports and Shopify Payouts - and the accountant's job is to reconcile every line of these reports against the bank deposit, the tax invoice and the GSTR-2B auto-populated TCS credit.
Key terms you need to know
Ecommerce Operator (ECO)
A digital platform such as Amazon or Flipkart that owns and operates the marketplace and is required to deduct TCS under Section 52 and TDS under Section 194-O.
Ecommerce Participant
The Indian seller listing goods or services on the operator's platform - this is your business.
TCS - Tax Collected at Source
1 percent of the net taxable value, deducted by the ECO and reflected in your GSTR-2B for credit in GSTR-3B.
Section 194-O TDS
Income tax deducted by the ECO at 0.1 percent (effective 1 October 2024) on gross sales, claimable in your ITR.
Settlement
The net amount paid by the marketplace into your bank account after all deductions - never the revenue figure.
Built for Section 24(ix) sellers.
Any business that supplies goods or services through an ecommerce operator must register under GST under Section 24(ix) of the CGST Act, irrespective of the Rs 40 lakh / Rs 20 lakh threshold. Specialist accounting support is appropriate for:
Six services, one CA-led engagement.
1. Multi-Platform Bookkeeping
- Daily entry of gross sales, returns, commissions, fulfilment fees, advertising deductions and refunds.
- Every transaction segregated by marketplace and SKU.
- Books designed for channel-wise margin analysis, not aggregated revenue.
2. Settlement Reconciliation
- Line-by-line match of Amazon MTR, Flipkart Sales Report and Shopify Payouts against bank deposits.
- Short payments and hidden fees surfaced in the monthly recon.
- Disputed deductions flagged for follow-up with the marketplace.
3. GST Compliance (GSTR-1, 3B, 9)
- Monthly filing with TCS credit claim from GSTR-2B.
- Annual return preparation and reconciliation against books.
- Section 34 credit notes raised for returns and refunds to reverse output GST cleanly.
4. Section 194-O TDS Reconciliation
- Match Form 26AS entries to platform sales line by line.
- Validate the 0.1 percent deduction (5 percent under 206AA if PAN/Aadhaar absent).
- Prepare the credit claim for your ITR.
5. Income Tax Return Filing
- ITR-3 or ITR-5 preparation with advance tax computation.
- Presumptive scheme evaluation under Section 44AD / 44ADA where eligible.
- Coordination of the 194-O TDS credit claim against the year's tax liability.
6. Monthly MIS and Profitability
- Channel-wise P&L (Amazon, Flipkart, Shopify split).
- Category-wise margin analysis, cash flow statement, and inventory valuation.
- MIS pack delivered by the 15th of every month with CA sign-off.
What lands in your inbox every month.
Six reports, delivered by the 15th, ready for founder review and auditor scrutiny.
- Channel-wise profit and loss statement (Amazon, Flipkart, Shopify split).
- Settlement reconciliation report flagging short payments, excess deductions and missing payouts.
- Monthly GST filing dashboard with TCS credit and ITC reconciliation.
- Form 26AS vs. books reconciliation for Section 194-O TDS.
- Inventory ageing and slow-mover report for stock kept under FBA, FAssured or self-fulfilment.
- Quarterly tax position memo including advance tax estimates.
Common ecommerce accounting challenges - and how we solve them
Challenge 1 - Settlement vs Gross Sales Confusion
Sellers record net settlement as revenue, understating GST liability and inflating margin. We map every line of the MTR to a ledger so revenue equals gross sales (ex-GST) and deductions hit the correct expense account.
Challenge 2 - TCS Credit Mismatches in GSTR-2B
Marketplaces sometimes report TCS late, causing credit to lag a month. We track period-on-period reconciliation and claim spillover credit in the next filing under the Section 52 framework.
Challenge 3 - Returns and GST Reversal Accounting
High-return categories like apparel can reach 30 percent returns; failing to reverse output GST inflates the liability. We process credit notes against the original tax invoice as per Section 34 of the CGST Act.
Challenge 4 - Multi-Platform, Multi-State IGST Exposure
Selling to customers across India creates IGST liability that must be place-of-supply-mapped. We use marketplace dispatch state data to apply correct CGST/SGST vs IGST and avoid notices.
Six steps from discovery call to first signed MIS.
Discovery Call
30-minute scoping call to confirm platforms, monthly order volume, GSTIN status and current accounting tool (Tally, Zoho Books or Excel).
Document Collection
Share GSTIN, marketplace seller-panel access (read-only), last 12 months bank statements and prior books via our secure portal.
Chart of Accounts Setup
Configure Zoho Books or Tally with ecommerce-specific ledgers - Sales by platform, Commission Expense, FBA Fees, Returns and TCS Receivable.
Settlement Integration
Import Amazon MTR (B2C and B2B), Flipkart Sales Report and Shopify Payouts; map every line item to the correct ledger.
First Monthly Close
Reconcile settlements to bank, file GSTR-1 by the 11th and GSTR-3B by the 20th, claim TCS credit from GSTR-2B.
Review and Sign-Off
Issue MIS pack by the 15th of every month with sign-off from a Regikart CA before delivery.
What you share at onboarding
Identity and access
- GST registration certificate (GSTIN) and login credentials.
- Marketplace seller-panel read-only access for Amazon, Flipkart, Meesho or others.
Financial inputs
- Last 12 months bank statements in PDF and Excel format.
- Prior year audited financials and ITR acknowledgement (if applicable).
- Form 26AS / AIS download for the current financial year.
Operating data
- Purchase invoices and vendor master from suppliers.
- Inventory list as on the start date with COGS values.
Transparent monthly pricing, scales with order volume.
Starter
1 platform, up to 100 orders/month
Growth
2 platforms, up to 500 orders/month, monthly MIS
Scale
3+ platforms, up to 2,000 orders/month, weekly recon
Enterprise
Multi-GSTIN, custom dashboards, dedicated CA
All fees and charges listed are indicative only and do not constitute a binding offer. Final amounts may vary depending on the volume of work and the complexity involved.
Get a fixed quote within 2 hours. Share platforms, monthly order volume, and current accounting tool and we will lock the plan.
Turnaround time
Books are closed within 7 working days of settlement receipt. GSTR-1 is filed by the 11th of the following month and GSTR-3B by the 20th, in line with the statutory due dates. The monthly MIS pack is delivered by the 15th. Late filing of GSTR-3B attracts late fees of Rs 50 per day (Rs 20 for nil returns), capped at Rs 5,000 per return per Section 47 of the CGST Act, plus interest at 18 percent per annum on unpaid tax under Section 50.
Why choose a specialist ecommerce CA team.
Recover hidden deductions
Line-level settlement reconciliation surfaces short payments and excess fees that aggregate reporting hides.
Avoid GST notices
Right TCS credit in the right period. No spillover, no duplicates, no Section 52 mismatches.
Stay audit-ready
Channel-wise books that match Form 26AS, GSTR-2B and the bank statement - every month, not at year-end.
Founder focus
Free the founder from accounting drudgery so the focus stays on listings, ads and supply.
Single point of contact
One CA who knows your platforms, your SKUs and your filing history - not a ticket queue.
“We sell on Flipkart and our own Shopify store and the cross-platform reconciliation was killing us. Regikart took it over in week one - one CA, one monthly fee, every settlement now matches the bank.”
D2C apparel brand, Pune
An apparel seller recovered Rs 1.8 lakh in short payments over 6 months through our settlement reconciliation process.
With offices in Kolkata, Delhi, Gurugram and Pune, Regikart serves ecommerce sellers across India - both in-person and remotely.
Generalist vs ecommerce specialist - line by line.
| Parameter | DIY / Generalist Accountant | Regikart Specialist Team |
|---|---|---|
| Settlement reconciliation | Manual, often skipped | Line-by-line, every period |
| TCS credit in GSTR-2B | Frequently missed or duplicated | Reconciled and claimed monthly |
| Section 194-O TDS | Rate confusion (1% vs 0.1%) | 0.1% post 1 Oct 2024 correctly applied |
| Multi-platform P&L | Single P&L only | Channel-wise margin reporting |
| Return / GST reversal | Often unrecorded | Section 34 credit notes raised |
| Audit readiness | Reactive - closed at year end | Audit-ready every month |
| Monthly cost | Rs 5,000 - 25,000 (in-house staff) | From Rs 3,499 (no hiring overhead) |
The statutes that govern marketplace sellers.
CGST Act 2017 - Section 24(ix)
Mandatory GST registration for every person making taxable supply through an ecommerce operator - irrespective of turnover. Intra-state goods exemption notified January 2023 for small suppliers below Rs 40 lakh.
CGST Act - Section 52 (TCS)
1 percent (0.5% CGST + 0.5% SGST) on net taxable value of marketplace supplies. Deductor files GSTR-8; credit reflected in seller's GSTR-2B for claim in GSTR-3B.
Income Tax - Section 194-O
0.1 percent on gross sales wef 1 October 2024 (Finance Act 2024). Threshold Rs 5 lakh for Individuals/HUFs with PAN or Aadhaar. 5 percent under Section 206AA where PAN is not furnished.
Late Filing - Sections 47 and 50 CGST
GSTR-3B late fee Rs 50 per day (Rs 20 nil) capped at Rs 5,000 (Section 47); interest at 18 percent per annum on unpaid tax (Section 50).
Official references: CGST Act 2017 (IndiaCode) · GST Portal · Income Tax Department.
GSTR-3B is due on the 20th of every month
Late filing attracts Rs 50 per day late fee under Section 47 of the CGST Act, plus interest at 18 percent per annum on the unpaid tax liability under Section 50. For sellers with growing volumes, even one missed filing can trigger a notice and block the e-way bill facility - making consistent monthly closure non-negotiable.
Ecommerce accounting - answered.
Questions, answered.
If you don't see your question here, write to us - a senior partner usually replies within a couple of business hours.
Still have questions?
Book a free 20-minute consult with a senior partner - we'll walk through your case and outline next steps.
Talk to a partner →Quick answers
- Q: Mandatory GST threshold for marketplace sellers?
- A: None - registration is required from the first sale.
- Q: TCS rate under Section 52?
- A: 1 percent (0.5% CGST + 0.5% SGST) on net taxable value.
- Q: TDS rate under Section 194-O?
- A: 0.1 percent of gross sales from 1 October 2024.
- Q: GSTR-1 due date?
- A: 11th of the following month.
- Q: GSTR-3B due date?
- A: 20th of the following month.
- Q: Starting fee at Regikart?
- A: Rs 3,499 per month for single-platform sellers.
What pairs well with ecommerce accounting
Pair ecommerce accounting with the following Regikart services for end-to-end compliance.
GST Registration
Mandatory first step for every marketplace seller under Section 24(ix).
GST Return Filing
Monthly GSTR-1, GSTR-3B and annual GSTR-9 filed on time.
Income Tax Return Filing
ITR-3 / ITR-5 with Section 194-O TDS credit reconciled.
Zoho Books Accounting
Settlement imports, GST inside the software, CA-led monthly close.
Close monthly books, reconcile every settlement, file with correct TCS and TDS - by one CA team.
Regikart's CA team has been serving online sellers on Amazon, Flipkart, Meesho and Shopify with documented turnaround and channel-wise reporting. We combine specialist marketplace knowledge with end-to-end CA-led compliance for ecommerce businesses scaling from first sale to multi-crore D2C.
Free 30-minute consultation. We respond within 2 hours.
Reviewed by CA & CS Team · Regikart · Last updated 26 May 2026 · Next review 26 August 2026