MosoFin · payment reconciliation, in plain words

Does Stripe match your books?

This skill checks that what your payment app — Stripe, Square or PayPal — says you were paid matches what your books say. It also catches the most common bookkeeping mistake with online sales.

The 20-second version

You give it a month. It compares your payment app with your books, line by line, and tells you whether they agree. If they don't, it shows you where and why, and suggests the fix for your bookkeeper. It never changes anything itself.

Where the money goes

A $100 sale never reaches your bank as $100

A customer pays you $100. The payment app keeps its fee1, holds the rest for a few days23, then sends it to your bank — usually bundled with other sales. Your books have to show all three pieces, even though they happen on different days.

Customer pays $100.00 your sale Payment app takes its fee the same day fee $3.20 Waiting room $96.80 held a few days Your bank $96.80 the payout charge holds sends
Example figures: $3.20 is Stripe's published US card rate, 2.9% + 30¢, on a $100 sale1. Square and PayPal publish different rates45, and your contract may differ. Stripe pays out to US banks about two business days later2; Square can deposit the next business day3. Accountants call the waiting room a "clearing account" — money the payment app owes you but hasn't sent yet. Stripe's payout reconciliation report tracks the same balance6.
The mistake it catches

Your profit looks right. Your sales are wrong.

Your bank only ever sees the $96.80 payout, so that's often what gets recorded as the sale. The fee is never recorded at all. Profit comes out the same, which is why nobody notices.

The payment app itself keeps the sale, the fee and the amount left over as three separate figures7. In the US, the Form 1099-K it sends the IRS reports the full $100, before fees and refunds8. The IRS treats fees and refunds as amounts you subtract on your return, not as smaller sales9. Record only the payout, and your sales won't line up with that form.

Recorded correctly

Sale and fee recorded separately
Sales$100.00
Processing fees$3.20
Profit from this sale$96.80
Cash in the bank$96.80
Sales and costs both show their true size.

The common mistake

Only the bank payout recorded
Sales$96.80
Processing fees$0.00
Profit from this sale$96.80
Cash in the bank$96.80
Sales are too low, fees are invisible — and the profit line hides it.
At 1,000 sales a month$3,200of sales and fees missing from your reports, every month
Over a year$38,400of sales a lender, buyer or investor never sees
Fees you can see$0so you can't check what you paid against the published rates145 or your contract

Same example figures as above, scaled up: 1,000 × $3.20 = $3,200 a month, × 12 = $38,400 a year. Confirm how your accountant wants fees presented.

How a run starts

It asks five questions before it looks at anything

  1. Use your MosoFin connection, or upload the files yourself?
    Either works. You don't need a subscription to use it.
  2. Which payment app — Stripe, Square or PayPal?
    Each one sends its money differently.
  3. Which month?
    It never assumes a period.
  4. Does your bookkeeper record each sale, or one entry per payout?
    Not sure? It will show you what's in your books, and you decide.
  5. Does your payment app ever hold money back?
    Held money is still yours, so it's shown separately.

Then it reads your answers back — "Checking Stripe against your books for September. Go ahead?" — and waits for your yes.

What you need

Connect once, or upload three files

Connected with MosoFin

Just say yes

  • It reads your books directly — no exporting
  • If Stripe is connected too, it reads both sides
  • You'll still be asked for the bank statement, the one thing it can't see
Uploading instead

Bring three files

  • Payout report from your payment app's dashboard (CSV)
  • Your books for sales, fees and the waiting-room account — an export or trial balance
  • Bank statement for the month (PDF or CSV)
What you get back

A straight answer, and the fix for your bookkeeper

Do they match?Yes or no, for the month — with the difference in dollars.
What's off, and whyEach gap explained in plain words: a fee not recorded, a refund in the wrong month, a payout that didn't arrive.
Suggested correctionsThe entries your bookkeeper would post. Suggestions only — you decide.
Where every number came fromYour books, the payment app, or a file you uploaded — so nothing is a guess.
What it never does
  • Never changes your books. It reads and suggests. A person makes every change.
  • Never moves money, issues refunds or touches your payment app.
  • Never guesses a number. If something's missing, it tells you what's missing.
  • Never reads anything before you say yes.
Words you'll hear

Five terms, in plain English

Payout
The lump sum your payment app sends to your bank, usually covering many sales at once2.
Processing fee
What the payment app keeps for handling a card payment145. A real business cost.
Chargeback
A customer disputes a charge with their card issuer. The payment is reversed, and the amount plus a dispute fee is taken from your balance10.
Waiting room
Money the payment app owes you but hasn't sent yet. Accountants call it a clearing account6. It should empty out every few days; if it keeps growing, something's wrong — that last rule is bookkeeping practice, not a published standard.
Reserve
Money the payment app holds back for a set time to cover possible refunds and disputes. It's paid out when the term ends, minus anything it had to cover11.
Sources

Where the facts on this page come from

The payment apps' own documentation and the IRS, as published when checked on 20 October 2026. Rates and timings change — follow the link for today's figure. What the skill does comes from the skill's own files.

  1. Stripe — PricingStandard US online card rate, 2.9% + 30¢ per successful charge.
  2. Stripe — PayoutsHow Stripe sends your balance to your bank; US accounts are paid on a 2-business-day schedule.
  3. Square — Transfer optionsStandard transfers arrive the next business day for payments taken before the cutoff.
  4. Square — Our feesSquare's published rates for in-person and online payments.
  5. PayPal — Business feesPayPal's published rates, including PayPal Checkout.
  6. Stripe — Payout reconciliation reportMatches each payout to the charges, refunds and fees in it, and shows the balance not yet paid out.
  7. Stripe API — Balance transactionEach transaction carries the gross amount, the fee and the net amount separately.
  8. IRS — Instructions for Form 1099-KThe form reports the gross amount of payments, without subtracting fees or refunds.
  9. IRS — What to do with Form 1099-KFees, refunds and similar amounts are accounted for on your return rather than reducing the reported gross.
  10. Stripe — DisputesA dispute (chargeback) reverses the payment; Stripe debits your balance for the amount and the dispute fee.
  11. Stripe Support — Reserves FAQA reserve holds part of your funds for a set term to cover refunds and disputes, then pays it out.
About this skill

This page explains merchant-and-payment-processor-rec, from the MosoFin finance skills library, MosoFin/mosofin-finance-skills on GitHub. It describes the current version, which asks five questions first and accepts uploads. Read the skill on GitHub →