Ecommerce Reconciliation: How to Reconcile Online Sales, Fees & Refunds
Marketplace fees, batched payouts, refunds, chargebacks. Here's how to reconcile it all without losing your mind -- or your margin.
If you sell through Shopify, Amazon, eBay, or any online marketplace, you already know the problem: the money that lands in your bank account looks nothing like the sales you actually made. Fees have been stripped out. Refunds have been deducted. Three days of orders have been lumped into one deposit. And if you sell across multiple channels, you're juggling several of these puzzles simultaneously. Standard bank reconciliation techniques fall apart because the relationship between a sale and a bank deposit is no longer one-to-one. This guide walks through exactly why ecommerce reconciliation is different, how to do it properly, and how to automate the parts that eat the most time.
Why Ecommerce Reconciliation Is Different
Traditional bank reconciliation assumes a fairly simple model: you invoice a customer, the customer pays, and the payment appears in your bank. One transaction in your books, one transaction in your bank. Match them, move on. Ecommerce breaks every part of that assumption.
The Five Complications
1. Batched Marketplace Payouts
Amazon, Shopify, and eBay don't transfer each sale to your bank individually. They accumulate sales over a payout period -- typically every two to fourteen days -- then send a single lump sum. A deposit of £4,217.83 might represent 73 individual orders spanning a week. Your accounting system recorded 73 separate sales. Your bank shows one deposit. Matching them requires decomposing that payout back into its constituent parts.
2. Fee Deductions
Every marketplace takes its cut before the money reaches you, and the fees come in layers. Shopify charges payment processing fees (typically 1.5-2% plus a fixed amount per transaction). Amazon layers marketplace referral fees (8-15% depending on category), per-item fees, and FBA fulfilment fees if you use their warehousing. eBay combines final value fees with promoted listings charges. These are all deducted from your payout, not billed separately -- so your bank deposit is always lower than your gross sales by the cumulative fee amount.
3. Refunds and Chargebacks
When a customer returns an item or disputes a charge, the marketplace deducts the refund from your next payout. This means a payout might include sales from this week but refunds from orders placed weeks ago. The timeline mismatch makes reconciliation harder because you're comparing figures from different periods within a single bank deposit. Chargebacks add another wrinkle: the marketplace may hold additional fees (typically £15-20 per chargeback) on top of the refunded amount.
4. Multi-Currency Transactions
If you sell internationally -- and most ecommerce sellers eventually do -- your marketplace reports sales in the customer's currency but converts to your settlement currency at their own exchange rate. The rate used is the marketplace's rate at the time of payout, not the spot rate at the time of sale. This creates small but persistent discrepancies that accumulate over hundreds of transactions. You'll see £247.60 in your bank where your sales records suggest £249.12 should have arrived.
5. Settlement Timing Differences
A sale on January 31st might not settle until February 4th. If your reconciliation period is monthly, that sale sits in January's books but appears in February's bank statement. Multiply this across hundreds of daily orders and the month-end cut-off becomes a significant source of temporary discrepancies. You need to track which orders fall into which payout cycle, not just which calendar month they were placed in.
According to marketplace seller surveys, the average multi-channel ecommerce business spends 6-8 hours per month on reconciliation. For sellers doing over £50,000 monthly across two or more channels, that figure can reach 15+ hours -- nearly two full working days.
Worked Example: One Month of Shopify Sales
January 2026 -- Reconciliation Summary
Let's walk through a realistic month. You run a Shopify store selling homeware. In January you processed 50 orders. Here's what the numbers actually look like when you sit down to reconcile:
| Item | Gross (£) | Fees (£) | Refunds (£) | Net (£) |
|---|---|---|---|---|
| Week 1 payout (12 orders) | 1,968.00 | -57.07 | 0.00 | 1,910.93 |
| Week 2 payout (15 orders) | 2,475.00 | -71.78 | -62.00 | 2,341.22 |
| Week 3 payout (11 orders) | 1,749.00 | -50.72 | -49.00 | 1,649.28 |
| Week 4 payout (12 orders) | 2,048.00 | -59.39 | -45.00 | 1,943.61 |
| January total | 8,240.00 | -238.96 | -156.00 | 7,845.04 |
Your accounting system should show £8,240 in gross revenue, £238.96 in payment processing expenses, and £156 in refunds (either as contra-revenue or a separate refunds account). Your bank statement should show four deposits totalling £7,845.04. If any of those figures don't reconcile, you know exactly which week's payout to investigate.
The critical check:
Gross sales (£8,240.00) minus fees (£238.96) minus refunds (£156.00) should equal total bank deposits (£7,845.04). If there's a discrepancy, it usually means a refund was processed in a different period, a fee was miscategorised, or a payout included a settlement adjustment you haven't recorded.
Step-by-Step Ecommerce Reconciliation Process
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Step 1: Download your marketplace payout report. Every platform provides a payout-level report that breaks down each bank deposit into its component sales, fees, and refunds. In Shopify, this is under Settings > Payments > View payouts. Amazon Seller Central has it under Payments > Statement View. eBay provides it through Seller Hub > Payments > Reports. Download the full month as a CSV.
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Step 2: Export your bank statement for the same period. Download the matching month from your bank as CSV, Excel, or PDF. If your bank only provides PDF statements, convert them to CSV first -- our PDF converter handles 17+ UK bank formats and produces clean, reconciliation-ready output.
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Step 3: Match payouts to bank deposits. Work through each payout entry in your marketplace report and find the corresponding deposit in your bank statement. The amounts should match exactly. If a payout shows £2,341.22 net, your bank should have a deposit for £2,341.22. Date offsets of 1-3 business days are normal -- the bank deposit date will lag behind the marketplace payout date.
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Step 4: Reconcile fees to your expense accounts. Sum the fees from each payout and verify they match the total posted to your payment processing expense account. If you sell on multiple platforms, break this down per channel: Shopify fees, Amazon fees, eBay fees. This also serves as a cost-of-sale check -- if your fee percentage suddenly jumps, you'll catch it here.
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Step 5: Handle refunds and chargebacks. Cross-reference each refund deducted from your payouts against your refund records. The tricky part: a refund processed on January 28th might be deducted from your February 3rd payout. Track refunds by the date they were processed, not the date they hit your bank. For chargebacks, record both the refunded amount and any dispute fee as separate line items.
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Step 6: Investigate any remaining discrepancies. If your figures still don't balance, check for: payouts that span a month boundary (partially in this month, partially in next), marketplace reserves or holds (Amazon is particularly fond of these), currency conversion differences on international sales, or promotional credits that offset against payouts.
For a business selling on a single channel with fewer than 100 transactions per month, this process takes roughly 2-3 hours if done manually. Once you add a second channel, the time nearly doubles because you're running parallel reconciliations that need to be combined at the bank level -- two marketplace payouts might land on the same day, so your bank shows a total that's the sum of both platforms' net settlements.
Multi-Channel Complications
If you sell on both Shopify and Amazon (or any combination of marketplaces), your bank statement becomes a blend of payouts from different platforms with different payout schedules and fee structures. A single day's bank activity might include a Shopify payout covering last Tuesday through Friday, an Amazon settlement covering the last fortnight, and a PayPal transfer from direct website sales.
The key to multi-channel reconciliation is reconciling each channel separately first, then verifying the combined total against your bank. Trying to match individual marketplace orders directly to bank deposits is a path to madness -- the aggregation layers make it impossible without first decomposing each platform's payout.
Pro tip: set up separate nominal codes for each channel's fees. "Amazon Seller Fees", "Shopify Payment Processing", "eBay Final Value Fees" -- keeping them distinct makes it immediately obvious which channel is costing you the most to sell through, and where fee increases might be eroding your margins.
Automating Ecommerce Reconciliation
Where Manual Effort Gets Wasted
Most of the time spent on ecommerce reconciliation isn't analytical work -- it's mechanical matching. Downloading exports, aligning date formats, hunting for the bank deposit that corresponds to this week's payout, summing fees across dozens of line items. These are exactly the tasks that automation handles well.
ReconcileIQ for matching:
Upload your marketplace payout report and bank statement as CSVs. ReconcileIQ handles the many-to-one matching that makes ecommerce reconciliation difficult -- it can match a batch of individual marketplace sales to a single aggregated bank deposit, accounting for fee deductions and date offsets. Smart matching uses configurable tolerances for timing differences and handles the net-versus-gross arithmetic automatically.
CodeIQ for categorisation:
Once your bank transactions are reconciled, they still need to be coded to the correct accounts in your bookkeeping software. CodeIQ learns your chart of accounts and the patterns in your transaction data. After an initial session where it analyses your general ledger history, it categorises new transactions in around two minutes -- splitting marketplace deposits into revenue, fees, and refunds across the correct nominal codes, classifying VAT correctly, and posting directly back to Pandle, QuickBooks, Xero, or Sage.
The combination means you go from raw marketplace exports and a bank statement to a fully reconciled, fully coded set of books without manually matching individual transactions. For a typical multi-channel seller doing 200-500 orders per month, our team sees this reduce reconciliation time from 6-8 hours to under 30 minutes, with fewer errors because the arithmetic is handled programmatically rather than in a spreadsheet.
Recording Ecommerce Transactions Correctly
The bookkeeping entries matter as much as the reconciliation itself. Getting the structure right from the start means your reconciliation is straightforward rather than an archaeology exercise.
The Right Way to Record Marketplace Sales
Record each sale at its gross amount as revenue. This is the price the customer paid, before any platform deductions. Your revenue line should reflect actual sales volume -- it's the number your VAT return is based on, and it's the number that tells you whether your business is growing.
Record marketplace fees, payment processing fees, and fulfilment fees as expenses. These are costs of sale. Post them to a dedicated account -- not lumped into "General Expenses" or "Sundries". You need to see exactly what each platform is costing you.
Record refunds as contra-revenue (reducing gross sales) or to a dedicated refunds account. Either approach works, but be consistent. The critical thing is that refunds reduce your revenue figure, not increase your expenses -- a refund is not a cost of doing business, it's a reversal of a sale.
When the marketplace payout arrives in your bank, it represents the net of all three: gross sales minus fees minus refunds. If your bookkeeping records all three components correctly, the bank deposit will reconcile cleanly every time.
Month-End Cut-Off for Ecommerce
The biggest recurring headache in ecommerce reconciliation is the month-end boundary. Orders placed on January 29th, 30th, and 31st might not settle until February 2nd or 3rd. This creates a timing difference: revenue is recognised in January (when the sale was made) but the cash arrives in February (when the payout settles).
The cleanest approach is to reconcile based on payout date rather than order date for bank matching purposes. Your revenue recognition still follows the order date -- that's the accounting standard. But when you sit down to check that your bank deposits match your records, group by payout date. Each payout is a self-contained bundle: the marketplace tells you exactly which orders, fees, and refunds make up that deposit. Match the payout to the bank entry, and the month-end cut-off issue resolves itself because you're comparing like with like.
Frequently Asked Questions
How do I reconcile ecommerce sales with my bank statement?
Download your marketplace payout report (Shopify, Amazon, or eBay) and your bank statement for the same period. Match each payout deposit to its corresponding bank entry, accounting for the fact that marketplaces deduct fees and refunds before settling. The bank deposit will be lower than gross sales because of these deductions. Work through each payout individually, verifying that gross sales minus fees minus refunds equals the net deposit.
How do I reconcile multi-channel ecommerce sales across different marketplaces?
Reconcile each sales channel separately before combining. Download the payout or settlement report from each marketplace (Amazon Settlement Report, eBay Payments Summary, your payment processor dashboard). Match each channel’s net deposits to your bank statement individually. Record gross revenue, fees, and refunds per channel so you can see true profitability by marketplace. Only after each channel balances should you reconcile the combined figures against your accounting platform.
What is the best ecommerce reconciliation software?
The best ecommerce reconciliation software handles batched payouts, automatically accounts for fee deductions, matches across date offsets, and supports CSV and Excel exports from all major marketplaces. ReconcileIQ does all of this with smart matching that handles the many-to-one relationship between individual sales and batched bank deposits. For automated transaction coding and posting, CodeIQ learns your chart of accounts and categorises marketplace transactions in minutes.
How do I account for marketplace fees and refunds in bookkeeping?
Record each sale at its gross amount as revenue. Post marketplace fees and payment processing fees to a dedicated expense account (e.g., "Payment Processing Fees" or "Marketplace Commissions"). Record refunds as contra-revenue entries that reduce your gross sales figure. This way your revenue line reflects true sales volume, your expenses show the real cost of selling through marketplaces, and the net figure matches your bank deposits.
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