Amazon Flipkart Seller Payment Reconciliation Software India

Amazon Flipkart Seller Payment Reconciliation Software India

Your festive-sale orders shipped. The payout landed. It does not match what Seller Hub said you sold, and the return deductions are still arriving. Flipkart seller payment reconciliation means tying every bank credit back to the orders, fees, returns and taxes inside it. Most people searching for Flipkart payment reconciliation want to know how to do it by hand, today, in Excel, before deciding whether to buy software.

This guide does that, and the job got bigger this month. Redseer estimates about ₹24,000 crore of GMV and 8–9 crore orders across Amazon, Flipkart, Meesho and Ajio in the first two days of the festive sales alone (8–9 Oct 2026, reported by YourStory). Each of those orders now sits in a settlement file. On top of that, both marketplaces added new penalties and fees in August and September.

Below: the reports to download from Flipkart and Amazon, how to match a NEFT or UTR credit to its order lines, an Excel match sheet with formulas, every deduction and where it hides, claim windows, a dispute-ticket template, and an honest test of when Excel stops being enough.

Flipkart seller payment reconciliation: the reports to download first

Reconciliation fails most often because people work from one report when the money is spread across several. Download all of them for the same date range before you open a formula.

On Flipkart Seller Hub, go to Payments > Previous payments, pick the period and use Request Download. The file arrives as a workbook with separate sheets, each holding a different kind of money:

• Orders: one row per order item, with the sale amount, each fee, and the NEFT ID of the payment it was settled in
• Non-Order SPF: Seller Protection Fund credits that are not tied to a normal sale
• Storage & Recall: warehouse storage and stock-recall charges, if you use Flipkart fulfilment
• Ads: advertising spend recovered from your payout
• TDS and Tax Detail: the taxes held back (more on these below)

Also pull the Orders report and the Returns report from Seller Hub for the same window. Flipkart's own API documentation lists the report types a seller can access: the Settled Transaction Report, Orders Report, Returns Report, Commission Invoice Report and P&L.

On Amazon Seller Central, go to Reports > Payments. Two views matter. Date Range Reports (the Transaction report) covers all activity in a period, including activity that has not been settled yet. All Statements gives you the settlement flat file for each settlement period, which is the file that adds up to an actual deposit. Menu labels can differ slightly on Amazon.in, so search the Payments page for these names if they do not match exactly.

Marketplace	Report	Use it for
Flipkart	Previous payments workbook	What each NEFT credit actually contained
Flipkart	Orders report	What you expected to be paid for
Flipkart	Returns report	Why a later payment went negative
Amazon	All Statements (settlement flat file)	Matching a deposit to its lines
Amazon	Date Range (Transaction) report	Seeing what is still unsettled

How to match a bank credit (NEFT or UTR) to its orders

Start from the bank: it is the only number you know for certain.

1. Export your bank statement for the period. Keep three columns: date, reference (UTR) and amount. Filter to credits from Flipkart or Amazon.
2. For Flipkart, each payment in Previous payments carries a NEFT ID. That is the same reference that appears as the UTR on the credit in your bank statement. This one key joins a bank credit to every line in the Orders, Non-Order SPF, Storage & Recall, Ads and TDS sheets settled in that payment.
3. For Amazon, each settlement flat file has a settlement ID, a period and a total deposit amount. The bank narration usually does not carry the settlement ID, so match on total amount and deposit date, then use the settlement ID to pull its lines.
4. Sum the lines for each credit. If the lines add up to the bank amount, that credit is reconciled at payment level. If they do not, you are missing a sheet.

Payment-level matching tells you the money arrived, not that it was right. That needs the order-level check below.

The Excel sheet for Flipkart seller payment reconciliation

Build one workbook with four tabs. Column names in the marketplace exports change between versions, so map them to these standard names when you paste.

Tab 1 – Bank: Date, UTR, Amount.
Tab 2 – Lines: stack every settlement sheet into one table: NEFT/Settlement ID, Order Item ID (Flipkart) or Order ID + SKU (Amazon), Line type (sale, commission, fixed fee, shipping, penalty, ads, TDS…), Amount (credits positive, deductions negative).
Tab 3 – Orders: from the Orders report, with Order Item ID, selling price, category and dispatch date. Add Expected payout, worked out from your rate card for that category and price band.
Tab 4 – Returns: Order Item ID, return type (RTO or customer return), return date, status.

Then the formulas (written for an Excel Table named Lines):

• Payment check, on the Bank tab: =SUMIFS(Lines[Amount], Lines[NEFT ID], [@UTR]) gives Settled total. =[@Amount]-[@[Settled total]] gives Difference, which should be zero.
• Actual per order, on the Orders tab: =SUMIFS(Lines[Amount], Lines[Order Item ID], [@[Order Item ID]]). Summing across all payments matters, because one order can appear more than once: a sale credit first, then a return reversal in a later payment.
• Gap: =[@Actual]-[@[Expected payout]].
• Return tag: =XLOOKUP([@[Order Item ID]], Returns[Order Item ID], Returns[Return type], "").
• Status: =IF([@Actual]=0,"Not yet settled",IF(ABS([@Gap])<=1,"OK",IF([@[Return tag]]<>"","Return – verify","Unexplained"))).

Filter Status to Unexplained. Everything else is correct, still on its way, or a return to verify. Say you ship 1,200 orders in a month: if 40 rows land in Unexplained, you now have 40 tickets to look into, not 1,200 rows.

Why is my Flipkart payment less than the order value?

A payout is smaller than the order value by design. The question is whether each deduction is the right one, at the right rate.

Deduction	Where it shows	What to check
Commission / referral fee	Orders sheet / settlement line	Rate for your category and price band
Fixed or closing fee	Orders sheet / settlement line	Amazon announced +₹1 (≤₹500) and +₹3 (>₹500) from 7 Sep 2026
Collection fee	Orders sheet (Flipkart)	Prepaid vs COD rate
Shipping and weight charges	Orders sheet / settlement line	Billed weight vs your packed weight
Penalties	Orders sheet or Non-Order lines	Flipkart ₹30 / ₹60 / ₹90 from 23 Aug 2026
Seller cancellation fee	Amazon settlement line	Graded % from 17 Aug 2026
Return deductions	Later payment, negative line	Return type and reverse-shipping fee
Ads, storage, recall	Their own sheets	Matches your ad console and stock
Reserve / "other charges"	Lump line	Ask for a line-item breakdown

The new penalties. From 23 Aug 2026, Flipkart charges ₹30 for missing a dispatch date, ₹60 for a seller-side cancellation and ₹90 for a delay followed by a cancellation (MediaNama; The Week). Amazon's seller cancellation fee from 17 Aug 2026 is graded by order value: 10% below ₹10,000, 8% for ₹10,001–50,000, 5% for ₹50,001–1 lakh and 2% above that, plus 18% GST. Cancellations made by the buyer are exempt. For amounts, exemptions and the GST maths, see our breakdown of Amazon Flipkart seller penalty charges in 2026.

Weight charges are the deduction sellers most often win back. If billed weight is above what you packed, dispute the courier weight discrepancy with photos taken at packing.

Zero commission does not mean zero deductions. Flipkart moved to zero commission on products under ₹1,000 from November 2025, and extended it to all of fashion from 8 Jul 2026 (Flipkart Stories). Amazon removed referral fees on more than 12.5 crore products under ₹1,000 across 1,800+ categories from 16 Mar 2026 (About Amazon India). Fixed, collection and shipping fees can still apply. Before you call a referral fee an overcharge, check that your category was in the eligible list.

Returns arrive late. A festive order paid in October can be clawed back in November. Knowing the difference between RTO and RVP tells you which fee to expect on each reversal. Returns cost money on both marketplaces, so it is worth working to reduce your RTO rate before the next sale.

Amazon payment reconciliation and the "other charges" line

Amazon payment reconciliation follows the same method, with one difference. The Date Range report includes activity that has not settled, so it will never equal a single deposit. Reconcile deposits against All Statements. Use Date Range only to see what is still pending.

The hardest Amazon line is a lump deduction with no breakdown. On Amazon's Seller Forums, Indian sellers have described "other charges" deductions of Rs 24,531 and Rs 56,126.70 (threads from around 2024), with support replies that read as automated. When you see one, filter the settlement file to that settlement ID and the "other" transaction types. Then open a case asking for a line-item breakdown, using the template below.

On timing: Amazon.in's seller blog describes settlements every 7 days, with funds reaching the bank in 2–3 working days (the post dates from 2017). Flipkart says payouts can come in as little as 7 days from dispatch, depending on seller tier, and press reports put the range at 7–15 days. Read your own cycle on the Payments page before deciding a credit is late.

TCS and TDS: money held back, not fees

Two lines are taxes, not charges, and you can claim them back against your own liability.

• GST TCS at 0.5% (0.25% CGST + 0.25% SGST, or 0.5% IGST), down from 1% since 10 Jul 2024 under CBIC Notification 15/2024–Central Tax. Many guides, including the earlier version of this page, still say 1%. It is 0.5%. It shows in your GSTR-2B / electronic cash ledger once the marketplace files GSTR-8.
• Income-tax TDS under Section 194-O at 0.1% since 1 Oct 2024 (TaxGuru), or 5% if the marketplace does not have your PAN. It shows in Form 26AS / AIS.

Reconcile both every month: total TCS and TDS in the Tax Detail and TDS sheets should match what appears in your GST portal and 26AS. If they do not match, the marketplace has not filed or filed wrong, and that is money you cannot claim until it is fixed.

Flipkart seller payment reconciliation and claim windows: SPF and SAFE-T

Reconciliation often surfaces a return that came back damaged, used or wrong. That is a protection claim, and it has a deadline.

Flipkart SPF. An undated Flipkart FAQ document puts the window at 14 days from when you receive the return. Third-party guides quote other numbers. Treat 14 days as the working assumption, and confirm it for each return under Payments > SPF in Seller Hub.

Amazon SAFE-T. We could not find an official India window. The figure of about 30 days that circulates online, and that this page previously repeated, has no Amazon source we could verify. Read the "Reply by" and "Appeal by" dates on Manage SAFE-T Claims for each case. Those dates are the only ones that count.

Either way, file within days of the return arriving, not at month-end close.

A dispute-ticket template that gets read

Support teams close vague tickets. A ticket built from your match sheet looks like this:

Subject: Incorrect [fee type] on Order Item ID [ID], payment [NEFT ID / Settlement ID]
Order: [Order ID / Order Item ID], dispatched [date], selling price ₹[x], category [y]
Line disputed: [fee name] of ₹[charged], payment dated [date]
Expected: ₹[expected] per [rate card / policy clause, with its effective date]
Difference: ₹[gap]
Attached: settlement extract showing the line, rate-card screenshot, packing photo or video if it is a weight or return dispute
Request: reverse ₹[gap] in the next settlement, or a line-item explanation

Raise one ticket per issue type, list every affected order in it, and record the ticket number in the Status column so the reversal can be matched when it lands.

Excel is enough when… an agent is worth building when…

Excel is enough when you sell on one or two marketplaces, the Unexplained filter comes back with a handful of rows, and one person can close the month in an afternoon. Save the sheet above as a template. You do not need software.

An agent (or Amazon reconciliation software) is worth it when the monthly close takes days, you sell across Flipkart, Amazon and more, export formats keep changing, and claim deadlines pass before anyone has looked. At that point the work is repetitive and rule-based: download, stack, match, flag, draft the ticket. That is the kind of job software does well, provided a person still approves what goes to the marketplace.

FAQs

How do I download the Flipkart settlement report?

In Seller Hub, go to Payments > Previous payments, choose the date range and click Request Download. The workbook includes Orders, Non-Order SPF, Storage & Recall, Ads, TDS and Tax Detail sheets, each payment tagged with its NEFT ID.

What is the difference between Amazon's Date Range report and the settlement report?

The Date Range (Transaction) report shows all activity in a period, including unsettled activity. The settlement flat file under All Statements covers one settlement period and adds up to an actual deposit. Reconcile deposits against the settlement file.

How do I match a UTR number to orders?

For Flipkart, the UTR on your bank credit is the NEFT ID in Previous payments. Sum every settlement line with that NEFT ID, then group by Order Item ID. For Amazon, match the deposit by amount and date to a settlement ID.

What are the TCS and TDS rates for Flipkart and Amazon sellers in 2026?

GST TCS is 0.5% (since 10 Jul 2024) and Section 194-O TDS is 0.1% (since 1 Oct 2024), or 5% without PAN. Both can be claimed against your own GST and income-tax liability.

Is reconciliation software worth it?

At low volume, a well-built Excel sheet is enough. Software or an agent pays off when the close takes days, you sell on several marketplaces, and claim windows are being missed.

What Cybiqon would build for this

For a brand selling a few hundred to a few thousand orders a month, Cybiqon would build a reconciliation agent around your exports. It would pull the Flipkart workbook and the Amazon settlement files, match each NEFT and UTR credit to its order lines, check fees against the rate card in force on that date, and flag Unexplained rows, missing TCS or TDS, and claim deadlines. It would also draft the dispute ticket, and a person approves each one before it is sent.

It is written for your business, not configured from a template. The founders build it, you own the code, and there is no per-order SaaS fee. AI agents start at ₹19,999 one-time, scoped on the first call.

The easiest way to see whether it is worth it: email support@cybiqon.in with one month's settlement export and we will tell you what an agent would flag. You can also book a 30-minute call or ring +91 9250711473.

Conclusion

Flipkart seller payment reconciliation is a method, not a product. Start from the bank credit, join it to the settlement by NEFT ID or settlement ID, compare actual against expected for each order, and work only the Unexplained rows. Know which deductions are fees, which are new penalties and which are taxes you can claim back. Check claim windows in the portal, not on blogs. If the festive-season close takes an afternoon, Excel wins. If it takes a week, send us one month's export and see what an agent finds.