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E-Commerce Accountants for Online Sellers in India

Reviewed by CA and CS Team, Patron Accounting LLP ICAI & ICSI Registered| 15+ Years Experience| Last Updated: July 2026 Verify Credentials →

Gross turnover you can defend: Your books carry gross sales, commission, shipping and returns as separate figures, so the turnover you report matches the portal.

TCS credit actually in hand: You claim the tax each marketplace collected once it shows in your electronic cash ledger.

Channel-wise contribution after deductions: You see commission, shipping, advertising, packaging and return costs sitting against the channel that incurred them.

Stock at fulfilment centres proved: We agree units lying at fulfilment centres to the operator's inventory report and show goods in transit apart.

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What E-Commerce Accounting Covers — Scope, Deliverables and Who It Suits

📌 TL;DR - E-Commerce Accounting Services at a Glance

An ecommerce accountant reconciles marketplace settlements to the rupee instead of accepting the payout total. Section 194-O TDS at 0.1% and GST TCS at 0.5% are tracked into your GSTR-2B. Patron matches each Amazon, Flipkart and Shopify settlement to its commission, shipping and return deductions. RTO stock is provisioned, not ignored. Works well for D2C brands and marketplace sellers across India.

What lands in your inbox after the close is a settlement-wise reconciliation: every marketplace payout broken into gross sales, commission, shipping and returns, tied back to the revenue posted in your ledger. Alongside it sit a channel-wise margin summary, a stock position covering both your warehouse and the fulfilment centres, and a dated trial balance. Each of these carries the period it covers on its face. Sellers filing across states usually add a multi-state reconciliation walkthrough.

Ecommerce accounting services here cover settlement reconciliation, stock and returns provisioning, GST and TDS workings, plus the close itself. Workload increases when you add another marketplace, take a registration in a further state, or push more SKUs through each month. A new state widens it again. Marketplace dispute recovery, and credits claimed via the central GST portal, are handled as separate work.

What Is E-Commerce Accounting?

Every marketplace settlement is a bundle of gross sales, commission, shipping recoveries and returns rolled into one net payout. An ecommerce accountant is the specialist who takes that payout apart and ties each part back to your ledger.

An ecommerce accountant does for an online seller what a general bookkeeper cannot. They reconcile each Amazon, Flipkart or Shopify settlement to the rupee, provision stock that came back as returns, and track the tax the operator withheld. Ecommerce accounting services of this kind treat the settlement report, not the bank credit, as the true record of what was sold and what was deducted. The result is a set of books where channel margin, stock position and net revenue can be defended line by line. In short, it is industry bookkeeping shaped around how online platforms actually pay their sellers. Marketplace tax collection and input claims are recorded here, but their filing and rates stay with the GST specialists, not this engagement.

Key Terms for E-Commerce Accounting:

What Is E-Commerce Accounting. Every marketplace settlement is a bundle of gross sales, commission, shipping

Who Needs E-Commerce Accounting in India?

An ecommerce accountant is for online sellers whose bank payout never equals the sale they invoiced. When commission, shipping, TCS and returns sit between those two numbers, the businesses below need every marketplace settlement broken down, not accepted whole.

  • Amazon and Flipkart sellers whose settlement report shows deductions they cannot tie back to any order.
  • D2C brands selling through their own Shopify or WooCommerce store, matching Razorpay and COD remittances to dispatched orders.
  • Meesho and multi-marketplace sellers claiming the GST TCS credit sitting in the electronic cash ledger.
  • Apparel and footwear labels where returned and RTO stock builds up faster than the books record it.
  • Sellers holding inventory at fulfilment centres like FBA across several states, needing that stock proved.
  • Online sellers registered under several GSTINs, filing across states every return cycle.
  • Growing D2C startups approaching a lender or buyer who wants turnover defended line by line.
  • Sellers where the operator deducts Section 194-O TDS at 0.1%, to be matched against booked sales.

The software and platforms we work with

Amazon
Flipkart
Shopify
Meesho
Myntra
Nykaa

Our E-Commerce Accounting Services

ServiceWhat We Do
Marketplace settlement reconciliationAmazon, Flipkart and Meesho settlement reports reconciled to booked sales, with commissions and fees split out so net payouts agree. Learn to reconcile marketplace settlement reports Monthly
Returns and RTO provisioningCustomer returns, cancellations and RTO recorded against the right supply, so reversed sales and restocked inventory are fairly stated Monthly
GST TCS credit reconciliationTCS collected by operators under Section 52 matched to your electronic cash ledger, so the credit you claim is actually in hand Monthly
Operator TDS reconciliationSection 194-O tax deducted by operators reconciled against booked sales using 26AS and AIS, so nothing sits unclaimed for online sellers Monthly
Gateway and COD settlement matchingRazorpay, PayU and Cashfree payouts plus COD remittances matched to own-website orders, so every gateway settlement reconciles to sales Monthly
Fulfilment stock and channel marginStock at FBA and Flipkart fulfilment centres tracked and channel-wise contribution reported, giving your ecommerce accountant a defensible turnover figure Monthly
Our Process

How E-Commerce Accounting Works — Our Process

How Patron delivers e-commerce accounting, step by step from onboarding to a clean monthly close.

Step 1

Settlement report reconciliation

Each marketplace settlement is broken back to gross sales, commission, shipping, TCS and returns, because the bank credit is only a net figure. Gross turnover in the books comes from the portal's tax report, never from the amount that landed.

Illustration for Settlement report reconciliation: Each marketplace settlement is broken back to gross sales, commission,
Step 2

Returns and RTO treatment

Returns, cancellations and RTO consignments are matched back to the original order so the credit note references the right supply. Goods that never physically came back are separated from goods received, because the two have different consequences.

Illustration for Returns and RTO treatment: Returns, cancellations and RTO consignments are matched back to the original
Step 3

TCS credit claim from operator

The tax collected by each operator under the e-commerce collection provisions is agreed to the statement it files, and the credit is then confirmed as accepted in the electronic cash ledger. Unaccepted or missing credit is taken back to the portal.

Illustration for TCS credit claim from operator: The tax collected by each operator under the e-commerce collection
Step 4

Operator TDS versus booked sales

Tax deducted by the operator on the gross amount of sales is compared with the turnover recorded per portal. A mismatch usually means the portal has reported sales the books have not picked up, and that difference is chased to the order.

Illustration for Operator TDS versus booked sales: Tax deducted by the operator on the gross amount of sales is compared
Step 5

Gateway and COD settlement matching

For own-website orders, gateway settlements are matched to orders with the discount charge shown as a cost rather than netted against revenue. Cash-on-delivery is tracked from courier remittance advice to bank, leaving unremitted collections visible.

Illustration for Gateway and COD settlement matching: For own-website orders, gateway settlements are matched to orders with
Step 6

Fulfilment centre stock control

Stock held at marketplace fulfilment centres is reconciled to the portal's own inventory report, with goods in transit shown separately. Lost, damaged and disposed units are matched to the reimbursement actually credited by the operator.

Illustration for Fulfilment centre stock control: Stock held at marketplace fulfilment centres is reconciled to the portal's
Step 7

Channel level contribution

Commission, shipping, platform advertising, packaging and return costs are pushed down to the channel and, where the data allows, the SKU. Only then does it become visible which listings are trading at a loss after all deductions.

Illustration for Channel level contribution: Commission, shipping, platform advertising, packaging and return costs are

Documents Required for E-Commerce Accounting

Marketplaces pay you net of commission, TCS and returns, so the gross figures exist only in the portal files and the settlement reports matter more than the bank credit.

  • Marketplace settlement reports (Amazon Payments/Settlement report, Flipkart Seller Settlement, Meesho payment file)
  • Order-level sales register / MTR (Merchant Tax Report) or GST report from each portal
  • Returns, RTO and cancellation report (courier return / customer return files)
  • GST TCS statement from the operator (GSTR-8 data / TCS certificate) and the electronic cash ledger TCS credit
  • Form 26AS and AIS showing Section 194-O TDS deducted by the operator
  • Payment gateway settlement statements (Razorpay, PayU, Cashfree) and COD remittance advices for own-website sales
  • Stock / inventory records including goods lying at marketplace fulfilment centres (FBA, Flipkart Assured)
  • Purchase invoices from suppliers and vendors
  • Bank statements for every current account, in PDF and Excel or CSV
  • Expense bills: advertising and platform ads, courier and freight, packaging, rent, professional fees
Client Portal

How You Work With Patron

Everything happens in one secure login. You can see your active services, the Patron team on your account, and anything still pending. Once you raise a request, it moves through the same clear steps every time, so you always know exactly where your work stands.

Secure client portal login screen
1

Sign in securely

Your books, documents and requests all sit behind one private, password protected login. The team handling your account is shown on screen, so nothing sensitive ever needs to travel over email or WhatsApp.

Service catalogue inside the client portal
2

Raise your request

Choose the service you need from the menu inside the portal, where the price is shown before you go ahead. Your request is logged the moment you send it, with no phone calls or reminder emails to wait on.

GST registration document checklist in the client portal, with an upload button beside each item
3

Share what the service asks for

For every service, the portal shows the exact documents it needs, each with its own upload button. The list shown here is the GST registration checklist. When a service needs nothing from you, it simply asks for nothing.

Live request tracker inside the client portal
4

We review, prepare and file

Once your documents are in, your team checks them, prepares the work and files it for you. A live tracker shows each stage as it happens, from review to processing to done, so you never have to ask where things stand.

Deliverables area of the client portal
5

Collect your finished work

Every completed return, computation and certificate is placed in your Deliverables area. You can open, print or download any of them as a PDF whenever you need a copy.

Common E-Commerce Accounting Challenges and How We Solve Them

ChallengeImpactHow Patron Accounting Solves It
Stock held in marketplace warehouses across several statesEach fulfilment state needs its own GST registration and stock ledger; unregistered stock blocks input credit.Our team keeps state-wise stock ledgers and raises stock-transfer invoices between fulfilment centres, so credit stays claimable.
Marketplace commission and fees carry GST that goes unclaimedInput credit on platform charges is left on the table, quietly thinning already narrow marketplace margins.Patron pulls each tax invoice from the seller panel and claims input credit on commission, shipping and fulfilment fees.
TCS collected by each platform must tie to your electronic cash ledgerUnmatched TCS overstates the credit you can use and triggers GST notices when the electronic ledger disagrees.We reconcile platform TCS statements to the electronic cash ledger; see how Section 52 TCS works.
COD collections remitted net and late by couriersSales book at despatch while cash lands later net of charges, hiding short or unremitted COD.Patron reconciles courier COD remittances to despatch records and chases every shortfall before it ages.
Blended sales across Amazon, Flipkart and your own siteOne combined profit and loss hides which channel actually earns, so loss-making listings keep running unnoticed.Our team builds a channel-wise profit and loss, splitting revenue, fees and returns by marketplace.

E-Commerce Accounting Fees

Fee ComponentAmount
Starter — one seller on a single marketplace with routine monthly ordersINR 3,499 per month
Excl. GST & Government Charges
Growth — extra marketplaces, higher settlement lines or added GST statesOn quote
Managed — multi-entity seller books with custom settlement and payout reportingOn quote

One seller on a single marketplace fits the INR 3,499 per month Starter plan, with GST-ready books and settlement postings. Adding marketplaces, monthly order volume or fresh settlement lines is what lifts the tier, so your ecommerce accountant scopes the quote to real transaction counts. Speak with an accounting specialist on +91 94594 56700.

Fees exclude GST and government charges. Final quote confirmed after a scoping review.

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.

Professional accounting and compliance charges are scoped to your number of entities, funding stage and monthly transaction volume, and are separate from statutory and government charges. Contact us for a detailed, fixed quote.

Get a free E-Commerce Accounting consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

E-Commerce Accounting Compliance Calendar 2026

ComplianceDue DateApplies To
TDS / TCS deposit (Challan ITNS-281)7th of every month (30 April for March)Every business that deducts tax at source on salaries, rent, contractor or professional fees
TCS return by e-commerce operators (GSTR-8)10th of every monthE-commerce operators collecting 0.5% TCS (0.25% CGST + 0.25% SGST) on supplies
GSTR-1 (outward supplies)11th of every month for monthly filersGST-registered businesses filing monthly returns
TDS under Section 194-O on e-commerce sales (0.1%)7th of the following monthE-commerce operators deducting TDS on participant sales
GSTR-3B (summary return and tax payment)20th of every month for monthly filersGST-registered businesses filing monthly; QRMP filers pay via PMT-06
Tax audit report (Form 3CA/3CB-3CD)30 September 2026Businesses crossing the Section 44AB turnover threshold
Income-tax return, audit cases31 October 2026Companies and audit-liable firms
Annual GST return GSTR-9 and reconciliation GSTR-9C31 December 2026GST-registered businesses above the annual-return and audit thresholds

For an online seller two monthly dates dominate: GSTR-8 TCS by the 10th and the 194-O TDS deposit, both tied to marketplace settlements. TCS now sits at 0.5% and 194-O at 0.1%. Patron reconciles each payout before the e-commerce filing so your GSTR-2B credit ties out. Get a filing-reminder schedule set up; call +91 94594 56700.

Key Benefits

Why Professional E-Commerce Accounting Matters

Gross turnover you can defend

Your books carry gross sales, commission, shipping and returns as separate figures, so the turnover you report matches the portal.

  • Figures taken from the portal tax report, not net bank credit
  • Order level sales register reconciled to settlement reports
  • Without the split, turnover understates what the operator already reported

TCS credit actually in hand

You claim the tax each marketplace collected once it shows in your electronic cash ledger.

  • Collected TCS agreed to the operator's GSTR-8 statement
  • Missing credit chased while the settlement file is still available
  • Without it, collected tax is quietly written off as cost

Channel-wise contribution after deductions

You see commission, shipping, advertising, packaging and return costs sitting against the channel that incurred them.

  • Costs tied to the channel and, where data allows, the SKU
  • True contribution shown even when the account payout looks positive
  • Without it, you scale listings that lose money every order

Stock at fulfilment centres proved

We agree units lying at fulfilment centres to the operator's inventory report and show goods in transit apart.

  • FBA and Flipkart Assured stock tied to the inventory report
  • Lost and damaged units matched to the reimbursement credited
  • Without it, unreimbursed shrinkage stays buried in cost of goods sold

Returns recorded against the right supply

We tie every return, cancellation and RTO to the order it reverses, so each credit note points at the right supply.

  • Goods that never came back kept apart from goods received
  • Without it, revenue holds sales that were reversed months ago

Operator TDS matched to sales

We compare the tax each operator deducted against the turnover your books recorded for that portal.

  • Section 194-O deduction at 0.1% checked against Form 26AS and AIS
  • Portal-reported sales chased to the order they belong to
  • Without it, portal-reported sales stay missing from your books

Why Businesses Choose Patron Accounting for E-Commerce Accounting Services

Five things a founder can check before handing over the books. Each is a claim with the proof behind it.

Marketplace settlements reconciled to the rupee

Every marketplace payout hides shipping, commission and RTO deductions. Over 15+ years our team has learned to reconcile Amazon and Flipkart settlements for D2C sellers, tying each credit back to the order behind it.

Section 194-O TDS at 0.1% and GST TCS at 0.5%

We credit the 0.5% GST TCS to your electronic cash ledger from the operator GSTR-8, and match the Section 194-O TDS at 0.1% to Form 26AS. Our 25,000+ filings make this monthly routine.

Amazon, Flipkart, Shopify and your 3PL feeding one ledger

Your existing platform stays in place, whether Zoho Books, Xero, Tally Prime or Odoo. We configure whichever tool you run so Amazon, Flipkart, Shopify and your 3PL feed one ledger.

Settlement-to-books reconciliation closed every payout cycle

You get a settlement-to-books reconciliation for every payout cycle, with each deduction identified and posted. The cadence is monthly, and the 4.9 star Google rating reflects sellers who now trust their gross turnover.

D2C and marketplace sellers among 3,000+ businesses

E-commerce sellers sit among the 3,000+ businesses we have served since 2019, from first-time sellers to established mid-sized groups. Backed by 15+ years of experience and a 4.9 star Google rating.

Figures reflect Patron Accounting LLP engagements since 2019. Scope and turnaround are confirmed in your engagement letter.

Marketplace Panel Reports vs Reconciled Books

CriterionMarketplace Panel ReportsReconciled Books
What it isSeller dashboard summaries from Amazon or Flipkart taken as the books directly.Ledgers built by matching settlement reports, bank credits and returns line by line.
Revenue recordedShows net payout after fees, understating true gross turnover for GST.Records gross sales, then fees, commission and TCS as separate line items.
Operator TCS and TDSGST TCS and 194-O operator TDS stay netted inside the payout.Operator TDS under 194-O at 0.1% and GST TCS are captured and claimed.
Returns and RTOReturn-to-origin and refunds net silently against sales, distorting the picture.Each return is recorded against its original supply, so revenue stays accurate.
Stock at fulfilment centresInventory lying in marketplace warehouses is not visible in the panel.Stock at fulfilment centres is tracked and valued in the books.
Compliance and audit riskUnderstated turnover invites GST mismatch notices and a weak audit trail.Books tie to GSTR filings and bank statements, lowering scrutiny risk.
VerdictPanel reports help operations but cannot serve as statutory books; gross turnover, TCS and returns must be reconciled. Any ecommerce accountant should treat settlement reconciliation as the base. See how to reconcile marketplace settlement reports.

Legal and Regulatory Framework for E-Commerce Accounting

What the law is protecting in e-commerce accounting is the integrity of a number the marketplace never shows you: your true taxable supply, before commission, shipping and returns are netted into a single payout. The CGST Act, the Income-tax Act and the accounting standards each reach that number from a different side, and an ecommerce accountant has to make them agree.

That is why the gross order value on a marketplace dashboard is only the starting point for the books. Tax is collected on it, deducted from it, and later adjusted for what the buyer sent back, so revenue is recognised net while the collected amounts are tracked as credits you reclaim. The Marketplace Settlement Reconciliation that sits behind the ledger is the mechanism that keeps the statutory figures below reconcilable to each payout.

  • Section 52, CGST Act 2017The marketplace collects GST TCS at 0.5% of net taxable supplies (0.25% CGST plus 0.25% SGST, or 0.5% IGST, since 10 July 2024) and reports it in GSTR-8 for you to claim - see Section 52 TCS under GST.
  • Section 194-O, Income-tax Act 1961The operator deducts income-tax TDS at 0.1% of the gross sale amount, which is credited against the seller's own tax liability. CBDT Circular 20/2021 sets out how 194-O, 194Q and 206C(1H) interact so one transaction is not taxed twice.
  • Section 24(ix), CGST Act 2017Sellers supplying through a marketplace generally take compulsory GST registration regardless of turnover, subject to the notified exemptions.
  • AS 9 / Ind AS 115 with Section 34, CGST Act 2017Revenue is booked net of returns, RTO and cancellations, with a GST credit note raised against the original supply - the accounting side of Return to Origin (RTO) Provisions.
  • Section 35(1), CGST Act 2017Accounts of stock, input tax credit and output tax are kept at the principal place of business and reconciled to the settlement reports.
  • Rule 3(1), Companies (Accounts) Rules 2014The edit-log audit trail stays enabled through the year, so corrections to a settled order remain traceable. Broader GST filing is handled on the hub page.

Practical note: During a GST review, the marketplace's GSTR-8 is routinely tallied against the TCS a seller has claimed, and unreconciled settlement reports are the most common reason a credit is held back.

Official sources: Ministry of Corporate Affairs · Income Tax Department · GST Portal · Startup India (DPIIT)

What is an e-commerce accountant?

An e-commerce accountant is a qualified accountant who reconciles marketplace settlement reports against your bank and books, then handles GST, TCS and TDS on online sales. The work differs from ordinary bookkeeping because Amazon, Flipkart and Meesho deduct commission, shipping, returns and penalties before payout, so gross sales never match the amount actually credited to you.

How are Amazon and Flipkart settlement reports reconciled with the books?

We download every settlement report, map each line to its order ID, and post commission, shipping, return and penalty entries separately instead of booking the net payout as sales. Reconciliation runs on a fortnightly cycle for most sellers, so differences are caught inside the same month. Unmatched lines are listed with the marketplace ticket reference raised.

How much GST TCS do marketplaces deduct and can it be claimed back?

Marketplaces deduct TCS at 0.5% of net taxable supplies under Section 52 of the CGST Act, split as 0.25% CGST and 0.25% SGST. The credit reaches your electronic cash ledger only after you accept the TCS statement on the GST portal. Many sellers never accept it, so the money sits unused for months.

What TDS does a marketplace deduct on online sales?

E-commerce operators deduct TDS at 0.1% of gross sales under Section 194-O of the Income Tax Act, and the deduction appears in your Form 26AS. We reconcile 26AS against marketplace reports every quarter so nothing is lost at return time. Where the deduction is wrong, we raise the correction before the quarterly statement is filed.

Is GST registration needed in every state where stock is held?

Yes. Holding stock in a fulfilment centre creates a place of business, so a seller using warehouses in five states needs registration in each of them. We handle the additional registrations, state-wise returns and stock transfer documentation. Sellers shipping only from their own single location usually manage with one registration instead.

How do you account for returns, RTO and lost shipments?

Returns and RTO are booked as credit notes against the original invoice in the same GST period wherever possible, never netted off against sales. Lost or damaged shipments are carried as claims receivable from the courier or marketplace until reimbursed or written off. We maintain an ageing of open claims so recoveries get chased rather than quietly absorbed.

What does e-commerce accounting cost for a seller doing Rs 50 lakh a year?

A seller at that turnover typically pays Rs 12,000 to Rs 20,000 a month, covering bookkeeping, settlement reconciliation for up to three marketplaces, monthly GST returns and TDS support. Pricing moves with order volume, number of marketplaces and number of GST registrations rather than turnover alone. Annual filings and tax audit support are quoted separately.

Can books two years behind across four marketplaces be cleaned up?

Yes. Backlog clean-up starts with a scoping review of about five working days, after which you get a fixed quote and a month-by-month catch-up plan. Historic settlement reports are pulled marketplace by marketplace and rebuilt from order level, so GST returns already filed can be corrected through amendments wherever the time limit still permits it.

Which accounting software do you use for online sellers?

We work in Zoho Books or Tally for most Indian sellers, with marketplace data brought in through settlement report imports rather than manual typing. QuickBooks is no longer available in India after Intuit withdrew the product in 2023, so sellers still on it are migrated to Zoho Books with full history carried across. Xero suits overseas entities.

Which account is best for an e-commerce business?

Use a dedicated current account for the business, kept apart from any personal savings account, with every marketplace payout credited into it so settlements can be traced to order level reports. Sellers running more than three marketplaces often add a second account for payment gateway receipts. In the ledger, each platform is kept as its own receivable control account rather than one combined debtor.

Quick Answers

What lands in your inbox after the close is a settlement-wise reconciliation: every marketplace payout broken into gross sales, commission, shipping and returns, tied back to the revenue posted in your ledger. Alongside it sit a channel-wise margin summary, a stock position covering both your warehouse and the.

E-Commerce Accounting Deadlines You Cannot Afford to Miss

TDS / TCS deposit (Challan ITNS-281) is due 7th of every month (30 April for March). TCS return by e-commerce operators (GSTR-8) is due 10th of every month. GSTR-1 (outward supplies) is due 11th of every month for monthly filers. Patron tracks each against your books so nothing is reconstructed after the fact. Call +91 94594 56700 to set up a filing-reminder schedule.

Start Your E-Commerce Accounting with Patron Accounting

Choosing an ecommerce accountant is really a decision about whose number you trust: the one the marketplace hands you, or the one your own books can defend line by line. One of those two is what your margin is calculated from, and only one survives a question from a lender or a buyer.

Peak season stops being an accounting event once ecommerce accounting services run on a fixed routine. Sale-week volume moves through the same steps as any other week, so the pack you receive after a festive month reads exactly like the one before it. You compare October against September on the same basis.

We begin by settling the channel list and file access: which marketplaces and gateways you sell through, and whether settlement files can be pulled for past periods. How your books record a returned sale comes next, just as our SaaS billing work starts with the contract file.

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E-Commerce Accounting Near You

Local teams for e-commerce accounting in these cities.

Reviewed by the CA & CS Team, Patron Accounting LLP
ICAI & ICSI registered  ·  15+ years in Indian accounting & compliance  ·  Last reviewed 23 July 2026  ·  Next review 23 October 2026