E-Commerce Accounting Services in India | Nainit Savla & Associates

E-Commerce Accounting Services

Q: What is TCS under GST for e-commerce sellers and how is it accounted for?

E-commerce operators deduct TCS at 1% on net taxable supplies. Sellers can claim it as GST cash ledger credit by reconciling with GSTR-8 filed by the marketplace. Missed TCS claims are a common compliance error.

Q: How do you reconcile marketplace settlements with our bank account?

We download settlement reports from each marketplace, reconcile gross sales, returns, fees, and TCS to derive the net remittance, match it to the bank credit, and post categorised entries to the accounting software.

Q: How should product returns and refunds be recorded in our books?

Returns reverse the original sale, reducing revenue and GST liability via credit note, and add the item back to inventory if resalable. Incorrect returns accounting is a major source of GST mismatches.

Q: Do D2C brands on Shopify need specialist e-commerce accounting?

Yes. Shopify accounting involves payment gateway reconciliation, COD reconciliation, discount accounting, return tracking, and multi-currency sales — none of which Shopify's native reporting handles for GST or management accounts.

Q: What GST compliance obligations does an Amazon seller have in India?

Amazon sellers must register in every state with FBA inventory, file GSTR-1 and GSTR-3B, file annual GSTR-9, and reconcile TCS from Amazon's GSTR-8 against their GST portal credits.

E-commerce businesses operate in one of the most accounting-intensive environments in the modern economy — high transaction volumes, multiple marketplaces, complex GST rules, TCS deductions, frequent returns and refunds, platform fee structures, and cash-on-delivery vs prepaid revenue splits. Our specialist e-commerce accounting service is built around the specific financial complexities of online selling — on Amazon, Flipkart, Meesho, Myntra, Shopify, and direct-to-consumer websites.

Marketplace Settlement Reconciliation

Detailed reconciliation of each marketplace settlement (Amazon, Flipkart, Meesho, Myntra) against sales reports, return reports, and bank remittances — every paise accounted for.

TCS Under GST — E-Commerce

Correct accounting of Tax Collected at Source (TCS) deducted by marketplace operators, reconciliation with GSTR-8 filed by the marketplace, and ITC claim verification.

Returns & Refunds Accounting

Accurate recording of product returns, refund adjustments, reverse logistics charges, and credit notes — ensuring the books reflect true net revenue and not gross sales.

Platform Fee & Commission Accounting

Recording of marketplace commissions, referral fees, fulfilment fees, advertising charges, storage fees, and other platform deductions as allowable business expenses.

Inventory Valuation

Tracking of opening and closing inventory, cost of goods sold computation, unsaleable or damaged stock write-offs, and FBA inventory reconciliation for Amazon sellers.

GST Compliance for Sellers

GSTR-1 and GSTR-3B filing for e-commerce sellers — with correct inter-state supply classification, HSN-wise reporting, TCS reconciliation, and GSTR-9 annual return preparation.

Why E-Commerce Accounting Requires a Specialist Approach

Standard bookkeeping practices designed for offline businesses are inadequate for e-commerce. A single month's Amazon settlement report may contain hundreds of individual transactions — sales, returns, FBA fees, advertising charges, storage fees, TCS deductions, and adjustments — that must be individually categorised, reconciled with GST data, and matched to actual bank deposits. Without specialist accounting, e-commerce businesses routinely overstate or understate revenues, miss TCS ITC claims, misclassify expenses, and create GST mismatches that attract notices.

Our e-commerce accounting service integrates with our outsourced bookkeeping and QuickBooks accounting capabilities to create a seamless, automated financial management ecosystem for online sellers.

Platforms and Marketplaces We Support

Amazon India (FBA and Self-Fulfilled) — settlement reconciliation and GSTR-8 matching
Flipkart — settlement reports, returns, and platform fee accounting
Meesho — reseller platform settlement and commission accounting
Myntra, Nykaa, Ajio — fashion and lifestyle marketplace accounting
Shopify India and international — revenue reconciliation and payment gateway settlement
WooCommerce — sales, refunds, and payment processor reconciliation
Etsy, Amazon Global Selling — cross-border e-commerce accounting in INR
Zomato and Swiggy — food delivery settlement reconciliation for restaurant businesses

Frequently Asked Questions

What is TCS under GST for e-commerce sellers and how is it accounted for?

Under Section 52 of the CGST Act, e-commerce operators like Amazon and Flipkart are required to collect Tax Collected at Source (TCS) at 1% (0.5% CGST + 0.5% SGST or 1% IGST) on the net value of taxable supplies made through their platform by third-party sellers. This TCS is deducted from the seller's settlement amount and deposited with the government. Sellers can claim the TCS as a credit in their GST electronic cash ledger by reconciling with the GSTR-8 filed by the marketplace operator. Correct TCS accounting and timely credit claim is a critical compliance step that is frequently missed by e-commerce sellers without specialist accounting support.

How do you reconcile marketplace settlements with our bank account?

We download the settlement reports from each marketplace (Amazon Payment Disbursement, Flipkart Settlement Report, Meesho Payment Report) and reconcile each settlement cycle against the gross sales, returns, platform fees, TCS, and other deductions to arrive at the net remittance amount. This is then matched to the actual bank credit. Discrepancies — such as pending reimbursements, deferred settlement cycles, or fee adjustments — are identified and followed up separately. The reconciled data is then posted to the accounting software with appropriate categorisation.

How should product returns and refunds be recorded in our books?

Product returns must be recorded as a reversal of the original sale — reducing both revenue and the related GST liability (through a credit note or return adjustment). The associated cost of goods returned must also be reversed to add the item back to inventory (if the product is resalable). Refunds that include marketplace-funded discounts or customer return protection credits must be distinguished from seller-funded refunds, as the accounting treatment differs. Incorrect returns accounting is one of the most common sources of GST mismatches in e-commerce books.

Do D2C brands on Shopify need specialist e-commerce accounting?

Yes. Shopify D2C brands have their own set of accounting complexities — payment gateway reconciliation (Razorpay, PayU, Cashfree), COD reconciliation through logistics partners, discount and coupon accounting, influencer marketing expense recognition, return rate tracking, and multi-currency accounting for international sales. Shopify's native reporting does not produce GSTR-ready data or management accounts — professional accounting support is needed to convert raw Shopify data into accurate financial records and GST-compliant books.

What GST compliance obligations does an Amazon seller have in India?

Amazon sellers in India must: (a) register for GST in every state where they store inventory (FBA sellers storing in Amazon's fulfilment centres must register in the state of each warehouse), (b) file GSTR-1 and GSTR-3B monthly or quarterly depending on turnover, (c) file GSTR-9 (annual return) and GSTR-9C (reconciliation statement for eligible sellers), and (d) reconcile TCS deducted by Amazon in their GSTR-8 against the TCS credit available in their GST portal. Multi-state registration is one of the most significant compliance burdens for FBA sellers and requires careful state-wise sales and tax computation.

Accounting Built for Online Sellers — Not Generic Businesses

Specialist e-commerce accounting for Amazon, Flipkart, Meesho, Shopify, and D2C brands — settlement reconciliation, TCS compliance, and GST filing done right.

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