Amazon and Flipkart Sellers: How to Keep Accounts and GST Under Control With BUSY Recom

Selling on Amazon, Flipkart or your own Shopify store brings orders from all over India. It also brings an accounting problem most traders have never faced: hundreds of small orders, payouts that never equal the sale amount, returns that come back weeks later, fees on every order, and taxes deducted by the marketplace before you are paid. Many sellers know their sales but cannot say, order by order, whether they were fully paid.

This guide explains where e-commerce accounting goes wrong, what GST and income-tax rules apply, and how BUSY with BUSY Recom, BUSY's e-commerce reconciliation plug-in, brings orders, returns, fees and settlements into one set of books.

The big challenges for online sellers

GST and tax rules every seller should know

• Registration: selling goods through an e-commerce operator generally needs GST registration. Small sellers within one state have limited relief under notified conditions, so check your case with your CA.
• GST TCS (section 52): the marketplace collects 0.5% of the net taxable value of your sales (0.25% CGST + 0.25% SGST, or 0.5% IGST) and reports it in its GSTR-8 by the 10th of the next month.
• Claiming TCS: after GSTR-8 is filed, the credit appears on the GST portal (TCS and TDS credit received). Accept it there; it goes to your electronic cash ledger and can pay GST. Book TCS as a receivable, not an expense.
• Income-tax TDS on payouts: marketplaces deduct 0.1% TDS on the gross sales they settle (section 194-O of the 1961 Act, continued under the Income-tax Act, 2025). Match it with Form 26AS / AIS and claim it in your return.
• GSTR-1: report every sale, including those through the marketplace, with credit notes for returns. Supplies made through an e-commerce operator are also shown separately against the operator's GSTIN.
• ITC on marketplace fees: commission, shipping and other fee invoices carry GST and appear in GSTR-2B; claim them like any other purchase.
• E-way bills: needed for stock moved to marketplace warehouses above the value limit, even when it is not a sale.

Rates, limits and section numbers change from time to time. Check the latest notification or your CA before acting.

One order, many entries: an example

A customer pays Rs 1,180 for an item (Rs 1,000 + 18% GST). Figures below are an example only; real fees depend on the marketplace, category and your plan.

Now multiply by every order in the month, add returns and refunds, and pay in weekly batches. That is why spreadsheets break down and why the payout must be matched order by order.

How BUSY Recom solves it

BUSY Recom is BUSY's plug-in for e-commerce sellers. As described by BUSY on busy.in, it connects Amazon, Flipkart and Shopify seller accounts (several accounts in one place) to BUSY and:

• Imports orders, payments and returns and posts sales, sales returns and stock in BUSY automatically, with batch, MRP and serial number tracking where you use them.
• Reconciles payments in one click: fulfilled, partly paid and pending settlements by order, date or SKU, including payments released and on hold.
• Books marketplace charges such as platform fees, courier charges and service fees as expenses.
• Handles returns: return invoices, stock verification and sales-return posting.
• Keeps GST in BUSY: GSTIN and HSN checks, GSTR-1 / 2A / 2B / 3B reconciliation and filing, e-way bill and e-invoice, from the same books.
• Reports: order-wise, SKU-wise and date-wise payment reports, outstanding, settlement and profitability reports, across companies.

BUSY lists BUSY Recom on a per-order plan that renews after the order limit or 360 days, whichever comes first, starting at 12,000 orders. Ask us for the current price and the plan that fits your monthly orders.

A month-end routine for online sellers in BUSY

1. Daily or weekly: sync orders and returns

   Let BUSY Recom bring in orders, cancellations and returns, so stock and sales in BUSY stay current for every marketplace.

2. Weekly: match payouts

   Reconcile each settlement with its orders. Follow up orders that are pending, short-paid or on hold, and file claims for lost or damaged returns within the marketplace's time limit.

3. Monthly: fees and ITC

   Check that every marketplace fee invoice is booked and that its GST appears in GSTR-2B. Bharat GST Champ matches GSTR-2B with your BUSY purchases and expenses, bill by bill.

4. Monthly: GSTR-1 and 3B

   File GSTR-1 from BUSY with returns as credit notes, then 3B. Accept TCS credit on the portal once the marketplace files GSTR-8.

5. Quarterly: TDS and stock

   Match TDS with 26AS / AIS, and count stock lying with each marketplace warehouse against BUSY.

Who should use it

• Sellers with a few hundred or more marketplace orders a month
• Brands and distributors selling on two or more marketplaces, or on Shopify plus marketplaces
• Sellers using marketplace warehouses in several states
• CAs and accountants who keep books for online sellers and need order-level proof

Get set up

Bharat Busy Care, an Authorised BUSY Platinum Partner, supplies BUSY and BUSY Recom, connects your seller accounts, sets up ledgers for fees, TCS and TDS, and trains your team in Hindi or English, online anywhere in India. Call or message us with your monthly order count and marketplaces.

Updated 2026-10-30 · Bharat Busy Care, Authorised BUSY Platinum Partner