What is e-commerce accounting and how is it different from regular bookkeeping?

E-commerce accounting records marketplace settlements, COD remittances, returns, RTO losses, platform fees, GST TCS, 194-O TDS and payment-gateway deductions at the order or settlement level. Regular bookkeeping often starts from the bank statement, but an online seller's bank receipt is already net of several deductions. That is why the books must rebuild gross revenue, fees, taxes and reversals before the P&L can be trusted.

Do online sellers need GST registration even below INR 40 lakh turnover?

Marketplace sellers generally need GST registration mandatorily under Section 24 of the CGST Act, regardless of turnover. The normal INR 40 lakh or INR 20 lakh threshold does not protect a seller supplying through e-commerce operators. For practical setup help, see our GST registration for e-commerce sellers service.

How do I claim the 0.5% TCS deducted by Amazon or Flipkart?

Marketplace operators deduct GST TCS at 0.5% and report it in GSTR-8. The seller must review and accept the TCS credit on the GST portal so it moves into the electronic cash ledger. We reconcile the marketplace report with sales, returns and GST filings before the credit is accepted.

What is Section 194-O TDS for e-commerce sellers?

Section 194-O requires e-commerce operators to deduct income-tax TDS on gross sales routed through the platform. The rate is 0.1%, with a higher rate if PAN is not furnished, and credit appears in Form 26AS or AIS. Good accounting captures this as a tax asset, not as a missing payout.

What is the Invoice Management System and does it affect my ITC?

The Invoice Management System lets recipients accept, reject or keep supplier invoices pending. From the October 2025 tax period, ITC is tied to accepted IMS records under amended Section 38, so inaction can become deemed acceptance. E-commerce sellers with high purchase volume need a monthly IMS review before filing.

How are returns and RTO recorded in e-commerce books?

Returns and RTO are recorded by reversing revenue, reversing or adjusting tax where permitted, and booking platform or logistics charges separately. The timing matters because a return may appear weeks after the original order. We connect order reports, settlement reports and courier data so the reversal lands in the right month.

Which accounting software works for Indian e-commerce sellers?

Tally, Zoho Books, QuickBooks-style workflows and ERP exports can all work if the marketplace data is normalized before posting. The software is less important than the chart of accounts, settlement mapping and review cadence. We adapt the workflow to the seller's volume, platforms and reporting needs.

How much do e-commerce accounting services cost in India?

Pricing usually depends on monthly order volume, number of marketplaces, D2C store volume, GSTIN count, payment gateways and whether historical cleanup is required. Starter sellers need basic monthly books and filing support, while scale sellers need reconciliations, MIS, SKU analysis and CA review. ComplyLocal uses order-volume tiers and confirms the final quote after reviewing platform access.

Do I need separate books for each marketplace?

You do not always need separate legal books for each marketplace, but you do need marketplace-wise ledgers and reconciliations. Amazon, Flipkart, Meesho, Shopify and payment gateways each deduct different fees and taxes. Marketplace-wise reporting helps verify payouts, detect fee leakage and prepare accurate GST and income-tax records.

What is ISD and why do multi-state sellers need it from 1 April 2025?

Input Service Distributor registration is mandatory from 1 April 2025 for businesses receiving common input-service invoices at head office and distributing ITC to GST registrations in other states. Multi-state e-commerce sellers often receive software, ads, logistics or consulting bills centrally. ISD helps distribute eligible credit to the right GSTIN instead of leaving it stranded.

How often should marketplace settlements be reconciled?

Marketplace settlements should be reconciled monthly at minimum, and high-volume sellers should review major platforms weekly. Waiting until year-end makes it difficult to trace fee changes, return reversals, TCS credit gaps and payment-gateway holds. A monthly close keeps books, GST returns and cash flow aligned.

Can ComplyLocal handle both my Shopify store and marketplace accounts?

Yes. We handle hybrid sellers that run Shopify or WooCommerce alongside Amazon, Flipkart, Meesho and other marketplaces. The workflow separates marketplace deductions, payment-gateway fees, COD cycles, refunds, ad spends and shipping costs, then reports them together in one MIS pack.

What happens if my GSTR-1 and GSTR-3B do not match?

A mismatch between GSTR-1 and GSTR-3B can trigger scrutiny or a DRC-01C-style intimation asking why reported outward supplies and paid tax do not align. Since GSTR-3B values are hard-locked from July 2025, corrections must be handled through the permitted return workflow. We reconcile sales, credit notes, returns and marketplace reports before filing to reduce that risk.

India's CA-led e-commerce accounting desk

E-commerce Accounting & Bookkeeping - Books That Match Every Settlement, Every Marketplace

Filed and reviewed by Chartered Accountants. Not by algorithms.

Settlement-true books for sellers on Amazon, Flipkart, Meesho, Shopify and hybrid channels, with monthly reconciliation, GST TCS, 194-O credits, returns, RTO and MIS handled together.

Marketplace, bank and books reconciled every month
GST TCS at 0.5% and 194-O TDS credits captured
Returns, RTO and platform fees booked separately
Monthly MIS reviewed by a CA-led team
Built for marketplace-only, D2C and hybrid sellers

Marketplaces we reconcile daily

D2C platforms

Logistics and payments

All marketplace and platform names are trademarks of their respective owners, shown to indicate the platforms we work with.

0.5%

GST TCS deducted on marketplace sales

Reconciled with GSTR-8 before credit acceptance

0.1%

Income-tax TDS under Section 194-O

Tracked into Form 26AS and AIS

Statements every order must reconcile across

Marketplace, bank and books

Services in the e-commerce compliance stack

Books, GST, tax, MIS, reconciliation and ROC

Which seller are you?

Different sales models need different accounting controls

We map the compliance stack to the way your revenue actually moves.

When

Marketplace-only seller

The issue

Payouts arrive net of commissions, shipping, ads, returns, GST TCS and 194-O TDS.

We do

Accounting, GST compliance and marketplace reconciliation work together.

When

Shopify or D2C brand

The issue

Payment gateways, shipping tools and COD remittances split one order into many cash events.

We do

Books, payment reconciliation and MIS show channel-wise margin.

When

Hybrid marketplace plus D2C

The issue

One stock pool sells through multiple platforms with different fees, return windows and taxes.

We do

Monthly books tie marketplace reports, D2C orders and GST filings together.

When

B2B plus e-commerce

The issue

Bulk invoices, online orders and state-wise GST registrations create mixed compliance risk.

We do

Accounting, GST return filing and tax compliance stay in one review cycle.

Online seller accounting

E-commerce Accounting Services Built for Indian Online Sellers

Our ecommerce bookkeeping services are built around settlements, not bank deposits. We map every marketplace payout back to gross sales, commission, shipping, ad deductions, GST TCS, 194-O TDS, returns and RTO, so the books explain the business instead of just recording receipts.

If you need an accountant for ecommerce business decisions, the monthly pack must show platform-wise revenue, fee leakage, tax credits and product contribution. ComplyLocal gives online sellers CA-reviewed books, filing support and MIS in one monthly rhythm.

Get a settlement review

What is e-commerce accounting?

E-commerce accounting is the bookkeeping discipline that records marketplace settlements, COD remittances, returns, RTO losses and platform fees at the order level, so your books tie to what Amazon, Flipkart, Meesho and Shopify actually paid you, not just what your bank statement shows.

As of FY 2025-26, online seller accounting also needs tight tax visibility. Marketplace settlements arrive net of commission, shipping, advertising, GST TCS and income-tax TDS under Section 194-O. If those deductions are posted as a single bank difference, revenue, tax credits and profitability all become unreliable.

Traditional bookkeeping starts too late for e-commerce. COD cycles run through aggregators, payment gateways settle after fees, and returns or RTO reversals can hit weeks after the original sale. We rebuild the settlement trail before posting entries, so GSTR-1, GSTR-3B, 26AS, AIS and the P&L can tell the same story.

E-commerce accounting and bookkeeping service with ComplyLocal

Complete compliance stack

One e-commerce desk for books, GST, tax and MIS

The hub keeps accounting as the source of truth, then routes specialized work to the right compliance page.

E-commerce cluster

Monthly GST return filing for e-commerce sellersState-wise GSTR-1 and GSTR-3B support built around settlement data.Marketplace payment and settlement reconciliationAmazon, Flipkart, Meesho, COD, gateway and bank reconciliation.E-commerce profitability analysisSKU, marketplace and fee-level margin analysis for better decisions.E-commerce MIS and reportingMonthly dashboards for sales, margin, cash, tax credits and growth.E-commerce tax and compliance support194-O, TCS, IMS, ISD, notices and income-tax support for sellers.

Shopify D2C accountingNextD2C books for payment gateways, COD, shipping, refunds and CAC.

Who this is for

Built for sellers whose books have outgrown spreadsheets

Amazon and Flipkart marketplace seller

You need settlement reconciliation, GST TCS credit capture, fee verification and state-wise GST liability every month.

Reconcile marketplace payouts

Shopify D2C founder

You need payment-gateway, COD, shipping, refund and ad-spend data posted correctly before you can trust margin.

Meesho or social-commerce reseller

You need low-ticket, high-volume orders cleaned into books without losing returns, claims or platform deductions.

Build monthly MIS

Multi-state seller with APOB registrations

You need books that split revenue, ITC, TCS, ISD and tax liability across GSTINs without creating mismatch notices.

Review APOB setup

Decision guide

Traditional accountant vs e-commerce CA

A normal accountant may close the ledger. An e-commerce CA has to close the settlement trail.

Factor	Traditional accountant	RecommendedComplyLocal e-commerce CA
Settlement reconciliation	Bank-entry ledgers	Marketplace, bank and books matched
TCS and 194-O credit capture	Often reviewed at year-end	Tracked monthly into GST cash ledger and 26AS
RTO and return accounting	Net adjustment only	Revenue, tax and logistics impact separated
State-wise GST liability	Manual split risk	GSTIN-wise sales, ITC and tax reviewed
Marketplace fee verification	Rarely checked	Commission, ads, shipping and penalties checked
MIS with ROAS and CAC	Basic P&L	Channel and SKU reporting for decisions

← Scroll →

Choose the accounting workflow that can explain marketplace payouts, not just bank receipts.

Talk to an e-commerce CA

Monthly workflow

How we close e-commerce books

A repeatable monthly close keeps filings, tax credits and management reporting aligned.

1
Onboarding and portal access
Step 1
We collect read-only marketplace, GST, banking and payment-gateway access, then map your platforms and GSTINs.
- Access checklist
- Chart of accounts
- Platform mapping
2
Historical cleanup
Step 2
Opening balances, unreconciled payouts, old TCS and 194-O credits, returns and fee ledgers are cleaned before monthly work begins.
- Prior period review
- Unclaimed credit scan
- Ledger cleanup
3
Monthly settlement-true bookkeeping
Step 3
We post gross sales, platform deductions, taxes, returns, RTO, COD remittances and gateway fees from settlement data.
- Order reports
- Settlement reports
- Bank matching
4
GST and TDS compliance loop
Step 4
Books are matched with GSTR-1, GSTR-3B, GSTR-8, 26AS, AIS and IMS before filings or credits are finalized.
- TCS acceptance
- 194-O tracking
- IMS review
5
Monthly MIS pack
Step 5
You receive channel-wise revenue, fees, tax credits, profitability, cash flow and exception notes.
- Marketplace MIS
- D2C MIS
- Exception report
6
Quarterly CA review call
Step 6
A CA reviews tax positions, profitability, working capital blocks and upcoming compliance actions with your team.
- Tax review
- Margin review
- Action tracker

What we need

Documents and access for e-commerce bookkeeping

Amazon, Flipkart, Meesho or other marketplace panel access, preferably read-only
Shopify, WooCommerce or D2C order exports
Marketplace settlement, return, fee and advertising reports

GST portal login and GSTIN-wise return history
Bank statements and payment-gateway dashboards
Form 26AS, AIS and prior income-tax return records where available

Shiprocket, courier or logistics reports
COD remittance records
Inventory, SKU master and product category mapping

Prior-year financial statements and trial balance
Existing accounting software backup or access
Open receivables, payables, loans and owner capital details

Access can be shared in stages. We start with read-only reports wherever possible and request sensitive logins only when required for compliance work.

The settlement gap

Marketplaces pay you net. Your books need the gross truth.

A payout is not revenue. We rebuild gross sales, platform fees, shipping, ads, GST TCS, 194-O TDS, returns and RTO from settlement reports so GSTR-1, 26AS and P&L agree.

Gross-to-net bridge

Every payout is broken into revenue, fees, taxes, deductions and reversals before posting.

Tax credit trail

GST TCS and 194-O are tracked as recoverable credits instead of vanishing into settlement differences.

Filing-ready books

Books are reviewed against return data before tax filings lock the month.

Review my settlement trail

Plans by order volume

E-commerce accounting plans

Pricing is tailored to your monthly order volume and scope. We confirm a fixed quote after a quick platform, GSTIN and cleanup review.

Starter

For early sellers who need clean monthly books and basic reconciliation.

Custom/mo

Up to 500 monthly orders
One marketplace or D2C channel
Monthly books and basic GST support
SKU profitability MIS

Ask for Starter quote

Popular

Growth

For sellers scaling across marketplaces with monthly reconciliation needs.

Custom/mo

500 to 5,000 monthly orders
Marketplace, bank and books reconciliation
GST TCS and 194-O credit tracking
Monthly MIS summary

Ask for Growth quote

Enterprise

For complex sellers with high order volume, multi-state GSTINs and custom reporting.

Custom/mo

50,000+ monthly orders
Multi-GSTIN accounting and ISD support
Custom MIS and exception workflows
Dedicated review cadence

Plan Enterprise workflow

DIY vs CA desk

Spreadsheets can track orders. They cannot close compliance.

E-commerce accounting needs controls around credits, returns, fees and filings.

Filing it yourself

Payouts are copied from bank statements without rebuilding gross revenue.
GST TCS and 194-O credits are checked late, so working capital stays blocked.
Returns, RTO and marketplace fee changes are hidden inside net settlements.
MIS is delayed because the source data is not reconciled first.

Filing with ComplyLocal

Marketplace, bank and books are reconciled before monthly close.
Credits, ITC, IMS, GSTR-8 and 26AS are reviewed in the same compliance loop.
Returns, RTO, COD, gateway fees and ad deductions are posted separately.
A CA-led review turns bookkeeping into decision-ready reporting.

Move to CA-led books

Problems solved

The issues we clean up for online sellers

The risk

Books never match marketplace payouts

Net payouts hide sales, deductions, taxes, refunds and claims in one number.

How we handle it

We create a gross-to-net bridge and reconcile marketplace, bank and books monthly.

The risk

TCS and TDS credits lying unclaimed

GST TCS and 194-O are recoverable credits, but only if they are tracked and accepted correctly.

How we handle it

We monitor GSTR-8, GST cash ledger, 26AS and AIS so credits do not disappear into expenses.

The risk

Notices from GSTR-1 vs 3B mismatch

Sales, credit notes and returns posted late can create filing differences.

How we handle it

We reconcile settlement reports before filing and create an exception note for differences.

The risk

No idea which SKU is profitable

Marketplace fees, ads, returns and shipping costs can erase margin without showing clearly in basic books.

How we handle it

We prepare MIS that shows channel and SKU-level contribution where data is available.

FAQ

E-commerce accounting FAQs

Answers to the questions Indian marketplace and D2C sellers ask before moving to a CA-led accounting desk.

Fast answersExpert support

E-commerce accounting records marketplace settlements, COD remittances, returns, RTO losses, platform fees, GST TCS, 194-O TDS and payment-gateway deductions at the order or settlement level. Regular bookkeeping often starts from the bank statement, but an online seller's bank receipt is already net of several deductions. That is why the books must rebuild gross revenue, fees, taxes and reversals before the P&L can be trusted.
Marketplace sellers generally need GST registration mandatorily under Section 24 of the CGST Act, regardless of turnover. The normal INR 40 lakh or INR 20 lakh threshold does not protect a seller supplying through e-commerce operators. For practical setup help, see our GST registration for e-commerce sellers service.
Marketplace operators deduct GST TCS at 0.5% and report it in GSTR-8. The seller must review and accept the TCS credit on the GST portal so it moves into the electronic cash ledger. We reconcile the marketplace report with sales, returns and GST filings before the credit is accepted.
Section 194-O requires e-commerce operators to deduct income-tax TDS on gross sales routed through the platform. The rate is 0.1%, with a higher rate if PAN is not furnished, and credit appears in Form 26AS or AIS. Good accounting captures this as a tax asset, not as a missing payout.
The Invoice Management System lets recipients accept, reject or keep supplier invoices pending. From the October 2025 tax period, ITC is tied to accepted IMS records under amended Section 38, so inaction can become deemed acceptance. E-commerce sellers with high purchase volume need a monthly IMS review before filing.
Returns and RTO are recorded by reversing revenue, reversing or adjusting tax where permitted, and booking platform or logistics charges separately. The timing matters because a return may appear weeks after the original order. We connect order reports, settlement reports and courier data so the reversal lands in the right month.
Tally, Zoho Books, QuickBooks-style workflows and ERP exports can all work if the marketplace data is normalized before posting. The software is less important than the chart of accounts, settlement mapping and review cadence. We adapt the workflow to the seller's volume, platforms and reporting needs.
Pricing usually depends on monthly order volume, number of marketplaces, D2C store volume, GSTIN count, payment gateways and whether historical cleanup is required. Starter sellers need basic monthly books and filing support, while scale sellers need reconciliations, MIS, SKU analysis and CA review. ComplyLocal uses order-volume tiers and confirms the final quote after reviewing platform access.
You do not always need separate legal books for each marketplace, but you do need marketplace-wise ledgers and reconciliations. Amazon, Flipkart, Meesho, Shopify and payment gateways each deduct different fees and taxes. Marketplace-wise reporting helps verify payouts, detect fee leakage and prepare accurate GST and income-tax records.
Input Service Distributor registration is mandatory from 1 April 2025 for businesses receiving common input-service invoices at head office and distributing ITC to GST registrations in other states. Multi-state e-commerce sellers often receive software, ads, logistics or consulting bills centrally. ISD helps distribute eligible credit to the right GSTIN instead of leaving it stranded.
Marketplace settlements should be reconciled monthly at minimum, and high-volume sellers should review major platforms weekly. Waiting until year-end makes it difficult to trace fee changes, return reversals, TCS credit gaps and payment-gateway holds. A monthly close keeps books, GST returns and cash flow aligned.
Yes. We handle hybrid sellers that run Shopify or WooCommerce alongside Amazon, Flipkart, Meesho and other marketplaces. The workflow separates marketplace deductions, payment-gateway fees, COD cycles, refunds, ad spends and shipping costs, then reports them together in one MIS pack.
A mismatch between GSTR-1 and GSTR-3B can trigger scrutiny or a DRC-01C-style intimation asking why reported outward supplies and paid tax do not align. Since GSTR-3B values are hard-locked from July 2025, corrections must be handled through the permitted return workflow. We reconcile sales, credit notes, returns and marketplace reports before filing to reduce that risk.

Related services

Keep the rest of your compliance connected

GST services

Tax services

Business setup

Make your marketplace books settlement-true

Send us your order volume and platforms. A CA-led e-commerce accounting specialist will review the right monthly workflow for your seller account.

Get accounting callback Chat on WhatsApp

For Amazon, Flipkart, Meesho, Shopify, D2C, COD and payment-gateway sellers.

E-commerce Accounting & Bookkeeping - Books That Match Every Settlement, Every Marketplace

Get e-commerce books reviewed

GST TCS deducted on marketplace sales

Income-tax TDS under Section 194-O

Statements every order must reconcile across

Services in the e-commerce compliance stack

Different sales models need different accounting controls

E-commerce Accounting Services Built for Indian Online Sellers

What is e-commerce accounting?

One e-commerce desk for books, GST, tax and MIS

Built for sellers whose books have outgrown spreadsheets

Amazon and Flipkart marketplace seller

Shopify D2C founder

Meesho or social-commerce reseller

Multi-state seller with APOB registrations

Traditional accountant vs e-commerce CA

How we close e-commerce books

Onboarding and portal access

Historical cleanup

Monthly settlement-true bookkeeping

GST and TDS compliance loop

Monthly MIS pack

Quarterly CA review call

Documents and access for e-commerce bookkeeping

Marketplaces pay you net. Your books need the gross truth.

Gross-to-net bridge

Tax credit trail

Filing-ready books

E-commerce accounting plans

Starter

Growth

Enterprise

Spreadsheets can track orders. They cannot close compliance.

Filing it yourself

Filing with ComplyLocal

The issues we clean up for online sellers

Books never match marketplace payouts

TCS and TDS credits lying unclaimed

Notices from GSTR-1 vs 3B mismatch

No idea which SKU is profitable

E-commerce accounting FAQs

01What is e-commerce accounting and how is it different from regular bookkeeping?

02Do online sellers need GST registration even below INR 40 lakh turnover?

03How do I claim the 0.5% TCS deducted by Amazon or Flipkart?

04What is Section 194-O TDS for e-commerce sellers?

05What is the Invoice Management System and does it affect my ITC?

06How are returns and RTO recorded in e-commerce books?

07Which accounting software works for Indian e-commerce sellers?

08How much do e-commerce accounting services cost in India?

09Do I need separate books for each marketplace?

10What is ISD and why do multi-state sellers need it from 1 April 2025?

11How often should marketplace settlements be reconciled?

12Can ComplyLocal handle both my Shopify store and marketplace accounts?

13What happens if my GSTR-1 and GSTR-3B do not match?

Keep the rest of your compliance connected

GST services

Tax services

Business setup

Make your marketplace books settlement-true

Documents and access for e-commerce bookkeeping

E-commerce accounting FAQs

01What is e-commerce accounting and how is it different from regular bookkeeping?

02Do online sellers need GST registration even below INR 40 lakh turnover?

03How do I claim the 0.5% TCS deducted by Amazon or Flipkart?

04What is Section 194-O TDS for e-commerce sellers?

05What is the Invoice Management System and does it affect my ITC?

06How are returns and RTO recorded in e-commerce books?

07Which accounting software works for Indian e-commerce sellers?

08How much do e-commerce accounting services cost in India?

09Do I need separate books for each marketplace?

10What is ISD and why do multi-state sellers need it from 1 April 2025?

11How often should marketplace settlements be reconciled?

12Can ComplyLocal handle both my Shopify store and marketplace accounts?

13What happens if my GSTR-1 and GSTR-3B do not match?