Stripe payout reconciliation tool

The Stripe gross-vs-net problem

Stripe deposits net of fees. Your invoice is gross.

You invoice a client $1,000. Stripe takes 2.9% + 30¢ = $29.30. The deposit in your bank account is $970.70. Your invoice is still marked $1,000.

If you try to reconcile by exact amount match — the standard approach — none of your invoices line up with any Stripe deposits. The match rate looks like 0% even though every invoice was paid.

This tool fixes that. Drop your Stripe payouts CSV and your invoice list, and the matcher handles the fee subtraction automatically. It also handles batched payouts (Stripe groups multiple invoices into a single deposit) and refunds (negative entries that reverse a previous match).

How to export your Stripe payouts CSV

1. In the Stripe Dashboard, go to Payments → Payouts.
2. Select the date range you want to reconcile.
3. Click Export → CSV (detailed).
4. Drop the resulting payouts.csv into the tool below.

Use the detailed export, not the summary one. The detailed CSV includes the per-transaction breakdown — that is what the matcher uses to associate individual charges with the parent payout.

How matching works for Stripe

The tool runs four passes:

1. Match each Stripe charge to an invoice by amount + customer email.
2. Group charges by payout_id to reconstruct what Stripe actually deposited.
3. Subtract Stripe fees from each charge to compute the expected net.
4. Sum the net amounts per payout and verify against the bank deposit (if a bank statement CSV is provided alongside).

The output:

• Invoices matched to specific Stripe charges → marked paid with the date of the underlying charge (not the payout date).
• Stripe charges with no matching invoice → flagged for review (refunds, disputes, or invoices missing from your export).
• Bank deposits matching reconstructed payout totals → confirms Stripe deposited what they said they would.

Why this matters for your books

Your accountant needs accrual-basis revenue (booked when invoiced) and cash-basis records (when actually deposited). Stripe’s dashboard shows you the latter but not the link back to your invoices. Without that link, your bookkeeping has a permanent gap between what your accounting software thinks happened and what your bank shows.

Reconciling Stripe payouts against invoices closes that gap. The numbers in your accounting tool should agree with both your invoice list AND your bank statement. If they don’t, you have a reconciliation problem hidden somewhere.

Common questions

Does it handle subscription renewals? Yes. Recurring charges are matched against the original invoice the same way one-time charges are. Each renewal creates a new charge, which the tool matches against the corresponding subscription invoice.

What about Stripe Connect / Marketplace payouts? Connect platform fees appear as separate line items. The tool detects them and excludes them from invoice matching (they are platform revenue, not customer payments).

Refunds? Refunds appear as negative entries in the payouts CSV. The tool reverses any prior match for the refunded charge and re-flags the original invoice as unpaid.

Disputes / chargebacks? Same treatment as refunds — the original match is reversed and the invoice is flagged for re-collection.

Related resources

• Bank reconciliation tool — for non-Stripe deposits
• Bank reconciliation glossary entry
• How to know if an invoice has been paid