Total the fee deductions in your settlement reports by fee head for the invoice period, then compare each head with the fee invoice. Explain differences caused by timing, credit notes and tax lines. Recompute any unexplained gap order by order against your seller agreement or rate card, and raise a dispute with evidence for genuine overcharges.
Why invoices and settlement deductions rarely match
A marketplace records its charges in two places. The fee invoice is a document-level record, usually raised for a period. The settlement report is a transaction-level record of what was deducted from each order before payout. Both describe the same money, but in different formats, on different dates and at different levels of detail.
Common reasons for gaps:
- The invoice period and the settlement cycle do not line up.
- Returns and reversals are netted in a later settlement or in a credit note.
- Fee heads are named differently in each document.
- Tax components (GST on fees, TCS, TDS) appear on separate lines or in separate documents.
- Genuine errors, such as a wrong commission slab or a wrong weight band.
Confirm how each tax line should be treated with your tax adviser, and do not assume the treatment is the same across marketplaces.
Gather the right documents first
Reconciliation fails most often because a document is missing. Collect these for the same period:
- Seller agreement and the current rate card, including any revisions you were notified about
- Fee invoices, with invoice number, date, period and GSTIN
- Settlement reports for every payout cycle that touches the period
- Order and sales report, plus the returns report
- Credit notes and debit notes issued by the marketplace
- Bank statement entries for the payouts received
Step-by-step: reconcile the invoice to the settlement
- Fix the period. Decide whether you are matching by invoice period or by order date, and stay consistent.
- Map fee heads. Build a small table linking each invoice line (for example commission, fixed fee, shipping) to the matching settlement column.
- Total the settlement deductions by fee head for the period.
- Compare with the invoice head by head and note the difference in each.
- Explain the differences caused by timing, credit notes, reversals on returns and tax lines. Tag each one as explained or unexplained.
- Recompute unexplained items order by order against the agreed terms.
- Tie the net to the bank. Sales less deductions, adjusted for holds and reserves, should equal the payouts received.
Common mismatches and what to check
| Symptom | Likely cause | What to check |
|---|---|---|
| Invoice higher than deductions | Invoice raised gross, with reversals settled separately | Credit notes and return reversals |
| Deductions higher than invoice | Charges deducted before invoicing, or an overcharge | Next period's invoice, then the order-level rate |
| Same order charged twice | Duplicate fee line | Order ID across settlement files |
| Fee differs by order | Wrong slab, category or weight band | Rate card and product master |
| Return charged but no reversal | Missed commission reversal | Returns report against settlement |
Check each charge against your agreed terms
A total that matches the invoice can still be wrong, because both documents may carry the same incorrect rate. Test the charge itself:
- Commission: is the right category and slab applied to each order?
- Fixed or closing fees: do they match the price band on the rate card?
- Shipping or logistics fees: is the weight or size band consistent with your product data?
- Return-related charges: are they applied only where your terms allow?
Find the applicable rates in your seller agreement, the marketplace's rate card and any revision notices. Do not rely on old numbers, since terms change. Confirm the latest version in your seller panel or with your account manager before raising a claim.
Log disputes and run it monthly
For each confirmed overcharge, record the order ID, the fee head, the amount charged, the amount expected under your terms, and the clause or rate card page you relied on. Attach the settlement row and the invoice line. Track each case as open, raised, accepted or rejected, and check later settlements for the credit. Note any time limit for disputes in your agreement and raise claims well within it.
Spreadsheets work at low volumes. As order counts grow, MarketplaceMetrics by Fundle can reconcile sales and settlements, check commissions and fees against agreed terms, and track returns and recovery cases. Myntra Excel reports are reviewed, and other marketplaces are in scope discussion. Pricing is a tailored quote.
Worked example
Illustrative example only. The figures below are made up and exclude GST for simplicity.
| Fee head | Invoice (₹) | Settlement deductions (₹) | Difference (₹) |
|---|---|---|---|
| Commission | 48,000 | 46,500 | 1,500 |
| Fixed fee | 9,000 | 9,000 | 0 |
| Shipping fee | 15,000 | 15,800 | -800 |
The ₹1,500 commission gap could be commission reversed on returned orders in the settlement. Match it to the returns report and any credit note. If it is explained, mark it closed.
The ₹800 shipping gap goes the other way: more was deducted than invoiced. Recompute those orders against the rate card. If a few orders were charged a higher weight band than your product data supports, log them as a dispute with order IDs and evidence.
Questions and answers
How often should I reconcile marketplace fee invoices?
Monthly is the minimum, aligned to invoice periods and your books. Brands with high order volumes often review each settlement cycle so errors surface while the dispute window is still open. Check your seller agreement for the time limit on raising claims.
Why does my settlement total not match the fee invoice?
Usually because of timing, credit notes, return reversals, tax lines or different fee head names. Map each head, total the deductions for the same period and tag each difference. Whatever stays unexplained should be recomputed order by order against your agreed terms.
Where do I find the correct commission and fee rates?
Use your signed seller agreement, the marketplace's current rate card and any revision notices sent to you. Rates change, so confirm the latest version in your seller panel or with your account manager before disputing a charge.
Can I reconcile fees without specialist software?
Yes, with spreadsheets, if volumes are small and reports are consistent. It gets slow as orders, returns and fee heads grow. At that stage, a tool that checks fees against your terms and tracks recovery cases saves repeated manual work.