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. It tells you whether they agree. If they don't, it shows you where and why. It also 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. It holds the rest for a few days23. Then it sends the rest to your bank, usually together with other sales. Your books have to show all three pieces, even though the pieces 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. Your contract may differ. Stripe makes US card funds available to pay out 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 the books often record that amount as the sale. The books never record the fee 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. If you record only the payout, your sales won't match 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 and fees are invisible. The profit line hides both.
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

These are the same example figures as above, scaled up: 1,000 × $3.20 = $3,200 a month, × 12 = $38,400 a year. Ask your accountant how they want to present fees.

How a run starts

It asks five questions before it looks at anything

  1. Use MosoFin as your data source, or upload the files yourself?
    MosoFin is the connection to your books (QuickBooks and the other platforms you link). With it, the skill reads the data from there. Without it, you upload the files. The checks are the same. You need no subscription.
  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 is in your books. Then you decide.
  5. Does your payment app ever withhold money?
    Held money is still yours, so the skill shows it separately.

Then it repeats your answers to you: "Checking Stripe against your books for September. Go ahead?" It waits for your yes.

What you need

Connect once, or upload three files

Connected with MosoFin

Just say yes

  • It reads your books directly. You do not export anything.
  • If you connect Stripe too, it reads both sides
  • It will still ask you 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, as 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?It answers yes or no for the month. It also gives the difference in dollars.
What's off, and whyIt explains each gap in plain words: a fee the books do not record, a refund in the wrong month, a payout that didn't arrive.
Suggested correctionsIt suggests the entries your bookkeeper would post. These are suggestions only. You decide.
Where every number came fromThe skill names the source of each number: your books, the payment app, or a file you uploaded. Nothing is a guess.
What it never does
  • It never changes your books. It reads and suggests. A person makes every change.
  • It never moves money, issues refunds or touches your payment app.
  • It never guesses a number. If something is missing, it tells you what is missing.
  • It 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. It usually covers many sales at once2.
Processing fee
What the payment app keeps when it handles a card payment145. It is 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 every few days. If it keeps growing, something is wrong. That last rule is bookkeeping practice, not a published standard.
Reserve
Money the payment app withholds for a set time to cover possible refunds and disputes. The payment app pays it to you when the term ends, minus anything it had to cover11.
Sources

Where the facts on this page come from

The sources are the payment apps' own documentation and the IRS, as they published it when MosoFin checked on 20 October 2026. Rates and timings change, so 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: Balances and settlement timeA US card payment made on Monday is available in your Stripe balance on Wednesday, 2 business days later. Your payout schedule decides only when Stripe sends available funds to your bank.
  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 reportThe report matches each payout to the charges, refunds and fees in it. It also shows the balance that Stripe has not sent yet.
  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-KYou account for fees, refunds and similar amounts on your return. They do not reduce 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, frequently asked questionsA 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 → Do you want the worked examples? Learn it step by step →