· Reviewed by Nimra Khalid
What is payment processor reconciliation?
Payment processor reconciliation is the work of proving that the money a processor or marketplace deposits equals your gross sales less its fees, refunds, chargebacks, reserves and adjustments for the same settlement period. Each payout is broken into its parts and posted so revenue, fees and sales tax are correct and the bank deposit matches to the cent.
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Payment processor reconciliation: what we do and how it runs
Payment processor reconciliation is the work of proving that the money a processor or marketplace deposits equals your gross sales less its fees, refunds, chargebacks, reserves and adjustments for the same settlement period. Each payout is broken into its parts and posted so revenue, fees and sales tax are correct and the bank deposit matches to the cent.
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What it is
Payment processor reconciliation is the work of proving that the money a processor or marketplace deposits equals your gross sales less its fees, refunds, chargebacks, reserves and adjustments for the same settlement period. Each payout is broken into its parts and posted so revenue, fees and sales tax are correct and the bank deposit matches to the cent.
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What you get
Payouts tied to sales, fees, refunds and reserves, not lump-sum deposits
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How it runs
A2X, Synder or Link My Books set up and checked by a named accountant
04 / 06 -
Discovery call
We list your sales channels, processors, currencies and monthly payout counts, and check what connector, if any, is already feeding your ledger.
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A named accountant, a backup and a team lead
Inside your own software, on a fixed close calendar, with a reply from a person within 1 business day. Call +1-657-777-0006 or start a quote.
Get a custom quote 06 / 06
Who it is for
Online store owners
You sell on Shopify, Amazon or your own site and the deposits never match the sales report. You want channel revenue, fees and refunds posted correctly every month.
SaaS and subscription businesses
Stripe payouts blend new subscriptions, upgrades, failed retries and disputes. You need deferred revenue and processor fees posted from the settlement data, not the bank line.
Restaurants, clinics and service firms
Square, PayPal or a card terminal settles daily with fees netted out. You want the daily sales summary, tips and fees reconciled without manual spreadsheets.
What's included
- Stripe, Shopify Payments, Amazon, PayPal and Square payout matching
- Etsy, eBay, Walmart and other marketplace settlements where you sell
- A2X, Synder or Link My Books connection set-up and mapping review
- Gross sales, fees, refunds and chargebacks posted from settlement data
- Rolling reserves and holdbacks tracked as a receivable until released
- Sales tax and VAT collected by the marketplace split from revenue
- Multi-currency payouts converted and exchange differences posted
- Clearing accounts cleared to zero every period
- Exception log worked weekly with a note on each open item
- Month-end payout variance report by channel
- Processor fee summary for margin review
Deliverables and KPIs
| Deliverable | KPI we report | Cadence |
|---|---|---|
| Payout reconciliation by channel | Payout variance of $0 between settlement reports and bank deposits | Monthly |
| Clearing account review | Every processor clearing account at zero or fully explained | Monthly |
| Exception log | No unmatched payout older than 14 days | Weekly |
| Reserve and holdback schedule | Reserve balance agreed to the processor dashboard | Monthly |
| Fee and refund summary | Fees, refunds and chargebacks reported by channel with a margin note | Monthly |
| Reviewer sign-off | Second accountant checks every channel before release | Monthly |
KPIs are what we measure and report, agreed per engagement. Service-level commitments are set in your agreement.
How it works
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Discovery call
We list your sales channels, processors, currencies and monthly payout counts, and check what connector, if any, is already feeding your ledger.
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Connector and mapping review
You grant accountant access to your ledger and read-only access to each processor. We set up or repair A2X, Synder or Link My Books and agree the account mapping with you.
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Dedicated accountant assigned
A named accountant, a backup and a team lead take over. The first cycle rebuilds the clearing accounts and clears any unmatched historical payouts.
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Match, log, review
Each week the accountant matches payouts under our ReconBot workflow and works the exception log. Each month the team lead reviews and you receive the variance report by channel.
Software we work in
How much does payment processor reconciliation cost?
Payout reconciliation is priced per sales channel and payout volume, as a flat monthly fee. Connector subscriptions such as A2X or Link My Books are billed to you directly by the vendor and are not marked up. Pricing depends on volume and scope, so we send a custom quote within 1 business day.
What moves the quote
- Number of channels and processors (Stripe, Shopify, Amazon, PayPal, Square, others)
- Payouts per month and whether they settle daily or weekly
- Currencies and marketplaces outside your home country
- Backlog of unreconciled payouts and clearing balances to clean up
Market benchmarks
| Market | Typical range | Source |
|---|---|---|
| US | E-commerce bookkeeping typically sits at the upper end of outsourced bookkeeping, $150 to $1,600 per month, plus connector fees paid to A2X or Synder | indinero, RadCity (2026) |
| UK | Fixed bookkeeping fees £100 to £1,500 per month; Link My Books and A2X billed separately by the vendor | UK provider pricing surveys (2026) |
| Canada | C$300 to C$2,000 per month for bookkeeping; most SMBs C$400 to C$800 | Outsource Bookkeeping CA, TheAccTaxCo (2026) |
| Australia | Fixed bookkeeping fees A$300 to A$1,500 per month | Australian bookkeeping fee surveys (2026) |
Third-party ranges for orientation, not our prices.
Get a custom quote No setup fee. Month-to-month.
Payment processor reconciliation for your industry
Case study
14 months of payouts reconciled
Case studyReconciling 14 months of Shopify and Amazon payouts
An online retailer in the northeastern US sold through its own Shopify store and on Amazon. Deposits landed in the bank as lump sums net of fees, refunds, chargebacks and reserves, and the owner had been booking each deposit as sales. Fourteen months in, the books showed revenue that matched neither platform report, and the retailer's tax preparer would not work from them. The owner engaged LedgerBPO for payment-processor reconciliation, e-commerce accounting and catch-up bookkeeping. A named accountant, a backup and a team lead reconciled every payout for the 14 months back to the settlement reports and the bank, then put a monthly routine in place so the gap did not reopen. This ecommerce bookkeeping case study covers the first three months of payout reconciliation.
- Months of unreconciled payouts140
- Sales channelsShopify and Amazon, unreconciledShopify and Amazon, reconciled monthly
Security and compliance
- Read-only or reporting-only roles on Stripe, Shopify and marketplace accounts
- We never issue refunds, change payout accounts or move money
- MFA on every login and a per-client access log reviewed monthly
Full control list on the security page and country rules on the compliance page. Certifications are listed only when held.
Frequently asked questions
How much do Stripe reconciliation services cost?
Pricing depends on volume and scope, and we send a custom quote within 1 business day. As a market reference, US outsourced bookkeeping for online sellers generally runs $150 to $1,600 per month (indinero, 2026), with connector subscriptions such as A2X or Synder paid to the vendor on top. The number of channels and monthly payouts is what moves our quote.
Why do my Stripe or Shopify deposits never match my sales?
Because a payout is a net figure. Gross sales less processor fees, refunds, chargebacks, disputes, reserves and sometimes marketplace-collected sales tax arrive as one deposit, often for a period that does not line up with the calendar month. Reconciliation breaks each payout back into its parts so revenue and fees are posted at gross and the deposit matches.
Do I need A2X, Synder or Link My Books?
For more than a handful of payouts a month, yes, one of them saves hours and reduces errors. A2X and Link My Books suit Shopify and Amazon sellers on QuickBooks Online or Xero; Synder covers Stripe, PayPal and Square well. We recommend one based on your channels, set it up and check the mapping. You hold the subscription.
How do you handle Amazon reserves and Stripe holdbacks?
We record reserves and holdbacks as a receivable from the processor when they are withheld and clear that receivable when the funds are released in a later payout. The reserve schedule is agreed to the processor dashboard every month, so your balance sheet shows money the processor owes you rather than missing revenue.
Can you handle refunds, chargebacks and disputes?
Yes. Refunds are posted against revenue in the period they occur, chargebacks and dispute fees are posted to their own accounts, and reversed disputes are tracked until the funds come back. The monthly fee and refund summary shows you the cost of each by channel so you can see where margin is leaking.
What about sales tax and VAT collected by the marketplace?
Marketplace facilitator tax collected and remitted by Amazon, Etsy or Shopify is separated from revenue and from the tax you owe yourself. Where you collect the tax, it is posted to the liability account and reconciled under our sales tax reconciliation service. Either way, revenue is never overstated by tax that passes through.
Do you reconcile multi-currency payouts?
Yes. Payouts in a foreign currency are converted at the rate the processor applied, and the difference between the sale-date rate and the payout rate is posted to exchange gain or loss. Stripe and PayPal balances held in other currencies are reconciled to the processor's own balance report at month-end.
My clearing accounts have large old balances. Can you clean them up?
Yes. Old clearing balances usually come from payouts posted as revenue, duplicate connector imports or a mapping change part-way through the year. We rebuild the clearing account from the settlement reports, document each adjustment, and hand a summary to your accountant. Clean-up is quoted as a separate project before the monthly service starts.
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