How it runs for marketing agencies and consultancies
The same workflow covers PayPal, Square and GoCardless where UK and Australian agencies collect direct debits.
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.
What we handle for marketing agencies and consultancies
- Split each Stripe payout into charges, fees, refunds and disputes
- Apply gross charges to invoices and fees to a processor expense account
- Post refunds and chargebacks against the original invoice, not as new expenses
- Reconcile PayPal and GoCardless settlements with the same ReconBot workflow
- Log every exception with a reason and clear it before month-end
The KPI that matters here
Every Stripe payout matched to the bank within 2 business days and processor fees reconciled to the monthly Stripe statement.
Agencies compliance notes
1099 contractor reporting
Agencies rely on freelancers, and the IRS requires Form 1099-NEC for nonemployee compensation above the annual threshold, which is $2,000 for payments made in 2026. We collect W-9s at vendor setup, code every contractor payment, and hand your preparer a reconciled 1099 report each January. Your firm reviews and files; we do not sign.
Retainers and deferred revenue
A retainer billed before the service period is a liability until the work is delivered. We keep a deferred revenue schedule that releases each retainer to income as hours are logged or the month ends, so your P&L matches the work actually performed.
WIP and unbilled revenue
Work delivered but not yet invoiced is an asset that lenders and buyers ask about. We reconcile unbilled hours from Harvest or your PM tool against the ledger monthly, so WIP is real, aged and collectible.
Gross versus net for media
ASC 606 and IFRS 15 ask whether the agency is principal or agent for media it buys on a client's behalf. We apply the treatment your CPA or accountant chooses and keep the pass-through account reconciled to platform statements so the answer is documented.
Agencies software we work in
More for marketing agencies and consultancies
Other services for agencies
Payment processor reconciliation in other industries
Frequently asked questions
Why does our Stripe balance never match the bank?
Because Stripe pays out net of fees on a rolling schedule, so a deposit rarely equals the invoices it settles. We reconcile at the payout level: the sum of charges, less fees and refunds, equals the deposit. Reconciling this way clears the bank line exactly and puts fees where you can see them on the P&L.
How do you handle a chargeback from a client?
The chargeback and its fee are posted against the original invoice so the client's balance reopens, and the case is logged as an exception. Your account lead decides whether to submit evidence through Stripe. If the dispute is won, the reversal is matched to the same invoice; if lost, the balance is chased or written off on your instruction.
Can you reconcile Stripe if we also invoice through QuickBooks Payments?
Yes, ReconBot handles more than one processor per agency. Each processor gets its own clearing account and payout workflow, and month-end includes a check that every clearing account is at zero. Multiple processors are common when an agency inherits clients from an acquisition or serves more than one country.
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