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Ecommerce Accounting for Amazon, Flipkart, Shopify & D2C Sellers

Online selling has changed the way modern businesses operate. But the accounting behind ecommerce is far more complex than traditional bookkeeping.
Multiple platforms, gateway settlements, shipping deductions, returns, RTO, commissions — everything must be reconciled precisely.

At Om Accounting, we provide ecommerce-specialized accounting designed for online sellers who want clarity, accuracy and profitability.

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The number in your bank is not your sales

This is the single most expensive misunderstanding in ecommerce accounting, and we see it almost every time a new seller comes to us.

Say Rs 8 lakh lands in your bank from a marketplace. It is natural to treat that as the month’s sales. It is not. Between the order and that bank credit, the marketplace has already taken its cut:

Gross sales → returns and refunds → commission → shipping and fulfilment → collection and payment fees → other adjustments → TCS and TDS → net settlement → bank credit

Only the last number reaches your bank. If your books are built on that number, then your sales are understated, your expenses are invisible, your GST working is wrong and your profitability is fiction — even though the P&L technically balances.

Our work is not entering transactions. Our work is reconciling that entire chain, month after month, so you know what you actually sold, what the marketplace actually charged you, what tax was actually deducted, and what you actually earned.

Where sellers usually are when they reach us

Very few come to us with no books at all. The usual position is subtler and harder: the transactions are recorded, but the marketplace settlements, the marketplace deductions, the operating expenses and the actual cash movement do not reconcile with each other.

For a multi-channel seller it compounds. In one business you will have marketplace collections, website sales, offline collections, raw-material purchases, job work, shipping, advertising and a dozen other operating costs running at the same time. The seller knows the sales figure. What is not clear is the contribution, the cash position, and which channel is actually making money.

In most cases that means three to six months of cleanup before the monthly cycle can run properly. In more tangled cases we have worked through six to twelve months of historical backlog before the opening position could be trusted.

What we handle right now

• 40+ clients, of which roughly 38 are ecommerce businesses
• Approximately 15–18 lakh order-level ecommerce transactions reconciled every month — higher during festive periods
• GST accounting and filing across roughly 60–70 GSTINs
• Amazon, Flipkart, Myntra, Meesho and D2C or website channels, including sellers running three or more platforms at once

Multi-channel is where the real difficulty sits, and it is not the volume. Every marketplace has its own settlement format, its own fee structure, its own returns logic and its own reporting cadence. Consolidating those into one honest picture — and then splitting profitability back out channel by channel — is the actual skill.

Why Ecommerce Accounting Needs a Specialist

Most small businesses can manage regular accounting.
Ecommerce sellers cannot.

Marketplace accounting involves:

• Order-level matching
• Fee & commission mapping
• Multi-channel settlements
• RTO & return adjustments
• Payment gateway reconciliation
• SKU-level profitability
• Inventory fluctuations

Even the smallest mismatch can distort your P&L.

Our team understands these challenges and delivers reconciliation-driven ecommerce books that give you complete clarity.

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Ecommerce Accounting Services We Provide

Marketplace Reconciliation (Amazon / Flipkart / Meesho / Ajio / Myntra)

We match every order with payouts, fees, commissions, and returns.
Short-payments and missing settlements are identified clearly.

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Shopify & D2C Accounting

• Razorpay / Cashfree / PayU / Stripe matching
• Refunds & chargeback accounting
• COD reconciliation
• Channel-wise sales & expense tracking

Perfect for D2C brands scaling through paid ads and multiple gateways.

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Monthly MIS Reports & SKU Profitability

You receive:

• Marketplace-wise Profit & Loss
• Cashflow insights
• SKU-wise profit analysis
• Expense breakdown
• Monthly performance dashboard

Clear numbers lead to clear decisions.

Virtual CFO Services

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Platforms We Support

We handle accounting for all major ecommerce ecosystems:

• Amazon (FBA/MFN)
• Flipkart
• Meesho
• Shopify
• WooCommerce
• Ajio / Myntra
• Nykaa
• Etsy
• UAE / US / UK online sellers

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Why Ecommerce Sellers Choose Om Accounting

• Dedicated ecommerce accountant
• Quick WhatsApp + call support
• Reconciliation-first approach
• SKU-wise & channel-wise clarity
• Transparent monthly pricing
• 100% secure & confidential
• GST-compliant books & on-time filing
• Works with Tally, Zoho Books, QuickBooks & Xero

We focus on accuracy and insight — not just bookkeeping.

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How Our Ecommerce Bookkeeping Process Works

One repeatable cycle, so nothing slips between marketplace, gateway and books.

Step 1 — Order & Sales Data Capture

Every sale is recorded at order level from Amazon, Flipkart, Shopify and your other channels.

Step 2 — Settlement Reconciliation

Payouts are matched line by line, deductions verified, and short-payments listed for recovery.

Step 3 — Expense Tracking

Ad spend, shipping, commissions and operating costs tracked separately so margin stays visible.

Step 4 — GST Management

Tax is calculated on reconciled figures and returns are filed on time.

Step 5 — Financial Reporting

Profit & loss, cash flow and channel reports, built only on verified data.

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GST for Ecommerce Sellers

Ecommerce GST differs from regular GST. Multi-state selling, varying category rates and returns change what you owe.

• Multi-state sales and place-of-supply treatment
• Different tax rates across product categories
• Return and refund adjustments reflected in your filings
• Marketplace deductions reconciled before filing

Filing on unreconciled numbers is the main reason sellers get notices. We file on matched figures.

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Problems We Fix for Online Sellers

• Payout mismatch — settlements that never equal recorded revenue
• Unknown real margin after commissions, ads, shipping and returns
• GST errors that become notices and penalties
• No channel or SKU reporting, so ad spend is guesswork

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Two reconciliations that found real money

These are our own client engagements, described without naming the businesses.

A seller at roughly Rs 1 crore annual turnover

During reconciliation we identified a previously unmatched amount of approximately Rs 1 lakh after working through the settlement reports, the books and the tax position together.

It is worth being precise about what that money was. It was not a bonus sitting somewhere. In cases like this the difference is usually a TCS credit that was never claimed, a remittance that never arrived and was never chased, a missing adjustment, or a marketplace deduction that was accounted incorrectly. You only find it by matching the chain end to end — not by matching the bank line.

Eight months of historical accounts

Another ecommerce client came to us with eight months of history in which the marketplace transactions and the books carried significant unmatched amounts. Detailed reconciliation surfaced a previously unidentified difference at the Rs 25 lakh level.

To be clear about the wording: that is the size of the mismatch we identified and accounted for, not a cheque that arrived. The more valuable outcome was structural — once the historical records were cleaned and the reconciliation process was standardised, the same class of mismatch stopped recurring in the months that followed.

A high-volume multi-channel business

An established seller was operating across marketplaces, a website and other channels. Volume was strong and collections were regular, but management could not answer a basic question: against these sales, what is the actual profitability and where is the cash?

Purchases, job work, shipping, marketplace costs and advertising were all landing in different places in the accounting data, while marketplace collections needed reconciling at settlement level. We mapped the whole trail — sales, marketplace deductions, net settlements, bank inflows, purchases, job work, shipping, advertising, other operating expenses, cash outflows — and then standardised a monthly reconciliation and reporting process on top of it.

The result was not a prettier ledger. It was that management could finally see, every month, whether sales were actually growing, which expense category was climbing, how much the marketplaces were deducting, and where the cash was going.

The three mistakes we correct most often

• Treating sales, settlement and cash as the same thing. They are three different numbers with a long chain of deductions between them. Reading only one of them is how a seller ends up confident and wrong.
• Judging profit by the bank balance. High sales do not automatically mean strong cash or good margins. Raw-material purchases, job work, supplier payments, advertising and shipping can move cash hard in a month that looked excellent on paper. P&L, settlement reconciliation and cash flow have to be read together.
• Skipping marketplace-wise reconciliation. When you sell on three or four platforms, consolidated bank entries make channel profitability almost impossible to see. One platform can be quietly funding another’s losses for months.

The tax numbers that decide your ecommerce margin

Current as of August 2026:

• GST TCS under Section 52 is 0.5% — 0.25% CGST plus 0.25% SGST intra-state, or 0.5% IGST inter-state. It was 1% until 10 July 2024. The marketplace deducts it before paying you and reports it in GSTR-8 by the 10th of the following month. That is your money: it lands in your electronic cash ledger and you claim it. Sellers who never reconcile GSTR-2A and GSTR-8 against their settlement reports routinely leave it sitting there.
• Income-tax TDS under Section 194-O is 0.1% of gross sales facilitated through the platform, down from 1% since 1 October 2024. Individuals and HUFs with PAN or Aadhaar on file are exempt below Rs 5 lakh of gross platform sales in a financial year; companies and LLPs are deducted from the first rupee. No PAN on file means 20%.
• Multi-state GST registration catches FBA sellers hardest. Stock held in a fulfilment centre makes that state a place of business, which means a separate GSTIN there — each with its own monthly returns. This is a large part of why we file across 60–70 GSTINs.

Rates and thresholds move. These are current as of the date on this page, and we tell our clients when they change rather than letting them find out from a notice.

How the month actually runs

Ecommerce accounting only works if it runs to a calendar, because the GST deadlines do not wait.

• By the 8th — we collect your marketplace and sales data. This cut-off exists so that GSTR-1 can be filed by the 11th without a scramble.
• By the 14th — bank and accounting data reaches us.
• 15th to 20th — reconciliation and GST work is completed and your monthly reporting pack is delivered.

What is in that pack:

• Profit & loss statement
• Balance sheet
• Marketplace-wise sales
• Marketplace settlement reconciliation
• Marketplace fees and charges analysis
• Returns and refunds analysis
• GST, TCS and TDS reconciliation
• Bank reconciliation
• Receivables and payables where applicable
• Inventory-related information
• Channel-wise profitability and management insights

The purpose is not to tell you the accounts are closed. It is so you can see how much you sold, how much the marketplace deducted, what your real gross and net margin were, and how the cash actually moved.

Onboarding: what it takes to start

If your books are clean, onboarding and reconciliation setup is generally structured within one to two weeks.

If there is a backlog of six months or more, we first standardise the historical marketplace, bank, GST and expense data, then run month-wise reconciliation and corrections. Depending on transaction volume and data quality that takes two to six weeks, sometimes longer.

On complex ecommerce businesses we deliberately choose a correct opening position over a fast one. Building monthly accounting on top of a wrong opening balance does not save time — it carries the problem forward and makes every month after it wrong too.

Who you are actually hiring

Om Global Accounting & Advisory was founded in Jaipur in July 2017 by Bhagirath Kirad, who holds a B.Com and an M.Com along with an MBA in Finance and Marketing. The firm is registered as an MSME, UDYAM-RJ-17-0475651.

We work with clients across India and overseas from our two offices in Jaipur — 201, Second Floor, 27B Dhuleshwar Garden, C-Scheme, and a second office in Patrakar Colony, Mansarovar Extension. Phone +91 80944 44888, email cs@omaccounting.in, Monday to Saturday 9 AM to 8 PM.

If you sell into India from overseas, or you are an accountant abroad whose client sells on Indian marketplaces, the same reconciliation work is available as a back-office engagement. See outsourced accounting services from India for how that is set up.

Get Clean, Accurate Ecommerce Accounting

Focus on growth, ads, and operations — while we handle every detail of your numbers.

Call: +918094444888

WhatsApp: +918094444888

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Frequently Asked Questions

Is settlement reconciliation really different from bookkeeping?

Yes, and it is the difference that matters. Bookkeeping records what happened. Settlement reconciliation matches gross sales through returns, commission, shipping, advertising, payment fees, adjustments and taxes down to the exact rupee that hit your bank. Books can look perfectly balanced and still be built on the wrong sales figure.

Do you work with sellers on more than one marketplace?

Most of our ecommerce clients sell on more than one, and several run three or more platforms at the same time. Each marketplace gets reconciled on its own terms and then consolidated, so you get one view plus channel-wise profitability rather than a single blended number that hides which platform is losing money.

What if I have six months or more of backlog?

That is a normal starting point, not a disqualification. We standardise the historical data first, then reconcile month by month. Two to six weeks depending on volume and data quality. We would rather take longer and hand you a correct opening position.

Can you find money I did not know was missing?

Sometimes, and it is a genuine part of the work rather than a promise. On one client at roughly Rs 1 crore turnover, reconciliation identified around Rs 1 lakh of previously unmatched amounts. On another, eight months of history carried an unmatched difference at the Rs 25 lakh level. Whether anything surfaces in your case depends entirely on your data — but nobody finds it by looking at the bank statement alone.

How many transactions can you handle?

We currently reconcile approximately 15 to 18 lakh order-level ecommerce transactions a month across our client base, and file GST across roughly 60 to 70 GSTINs. Festive months run higher.