The short answer: The most common reason your deposits don't match your invoices is that the processor batches a day's payments into one deposit and takes its fees out first. One-to-one settlement sends one deposit per payment, so each deposit matches one invoice.
For instance, a customer pays a $1,250 invoice by card on Monday. On Wednesday your bank shows one deposit of $6,008.45. It arrived together with another customer's $4,800 payment, and the processor took its fees out of both. No line on the statement equals either invoice.
Tool by tool:
- Stripe: Pays out your available balance on a schedule, net of fees, refunds and disputes. One payout can hold dozens of payments.
- Square: Sends one transfer per close of day, with its processing fees already taken out.
- QuickBooks Payments: Combines each day's payments into one deposit. QuickBooks Online books the batch and the fee for you, but the bank still shows one line for the day.
- Nickel: By default, sends each customer payment to your bank on its own, for the full invoice amount. ACH is free and the card fee comes out as a separate withdrawal.
Batch deposits vs one-to-one settlement
| Batch deposits | One-to-one settlement | |
|---|---|---|
| What hits the bank | One deposit per payout, net of fees, refunds and disputes | One deposit per customer payment, for the amount of that payment |
| What you reconcile | One lump sum against several invoices, using the processor's payout report | One bank line against one invoice |
| Where fees show up | Taken out before the deposit lands. QuickBooks Payments is the exception and shows its fee as a separate withdrawal | Not in the deposit. With Nickel, ACH is free and the card fee is its own withdrawal |
| How it looks in QuickBooks | One bank-feed line matched to several payments plus a fee, usually through Undeposited Funds | Each payment is already applied to its invoice, and the bank-feed line matches it for the same amount |
| Refunds and returns | Netted into the next deposit | Their own lines on the statement |
| Best fit | Many small sales a day: retail, food, point of sale | Fewer, larger invoiced payments: contractors, trades, distributors, manufacturers |
Why a batched deposit never equals an invoice
Three things happen between a customer paying and the money landing:
- The processor holds the payment until a daily cutoff and groups it with everything else that settled that day.
- It takes its fee out of each payment.
- It folds refunds, disputes and adjustments into the same balance.
Stripe publishes a payout reconciliation report for exactly this. It lets you "reconcile each payout with the batch of transactions it settles."
So the deposit is a day's sales minus fees, plus or minus whatever else moved. It isn't wrong, but it isn't an invoice.
A week of 6 payments, both ways
Say 6 customers pay 6 invoices in one week, 3 by ACH and 3 by card.
| Day paid | Invoice | Method | Amount |
|---|---|---|---|
| Monday | #1041 | ACH | $4,800.00 |
| Monday | #1042 | Card | $1,250.00 |
| Tuesday | #1043 | Card | $2,375.00 |
| Thursday | #1044 | ACH | $6,200.00 |
| Thursday | #1045 | Card | $980.00 |
| Friday | #1046 | ACH | $3,150.00 |
| Total | 6 invoices | $18,755.00 |
As batched deposits
Each business day's payments go out together, net of fees, and land 2 business days later.
| Lands | Bank statement line | What's inside |
|---|---|---|
| Wednesday | Deposit $6,008.45 | #1041 and #1042, less $41.55 in fees |
| Thursday | Deposit $2,305.82 | #1043, less $69.18 |
| Next Monday | Deposit $7,146.28 | #1044 and #1045, less $33.72 |
| Next Tuesday | Deposit $3,145.00 | #1046, less $5.00 |
| Total | $18,605.55 | $18,755.00 invoiced, $149.45 in fees |
Not one of the 4 bank lines equals any of the 6 invoices. To close the week, you:
- Open the payout report and find which invoices sit in each deposit.
- Record each payment to Undeposited Funds.
- Build a deposit in QuickBooks with the fee as a negative line, so it equals the bank amount.
- Match it in the bank feed.
Then you do it 4 times, every week.
As one-to-one deposits
Each payment goes to your bank on its own. ACH is free, so those deposits equal the invoice to the cent. Card fees, at Nickel's 2.9% flat rate, arrive as their own withdrawals.
| Bank statement line | Matches | Fee line |
|---|---|---|
| Deposit $4,800.00 | Invoice #1041 | None. ACH is free |
| Deposit $1,250.00 | Invoice #1042 | $36.25 withdrawal, separate |
| Deposit $2,375.00 | Invoice #1043 | $68.88 withdrawal, separate |
| Deposit $6,200.00 | Invoice #1044 | None |
| Deposit $980.00 | Invoice #1045 | $28.42 withdrawal, separate |
| Deposit $3,150.00 | Invoice #1046 | None |
| Total $18,755.00 | 6 invoices | $133.55 in 3 fee lines |
That's 6 deposits for 6 invoices, at the same amounts. Each payment was applied to its invoice in QuickBooks when it came in. When the bank line arrives for the same amount, QuickBooks pairs it with the payment on record and you confirm the match. The 3 card fees are 3 lines booked to one expense account. No payout report, no Undeposited Funds, no deposit to rebuild. For whoever closes the books on Friday, that's 6 matches to confirm instead of 4 deposits to take apart.
How Stripe, Square and QuickBooks Payments pay out
All three batch by default. Here's how each one groups payments, when the money lands and where the fee goes.
| How payments are grouped | When the money lands | Where the fee goes | |
|---|---|---|---|
| Stripe | Your available balance, paid out on a schedule such as daily | US payments become available 2 business days after capture | Taken out before the payout |
| Square | Everything up to your close of day, 5 PM PT by default | The next business day before the cutoff, or the second business day after it | Taken out before the transfer |
| QuickBooks Payments | Each day's invoice payments and sales receipts, as one deposit | Next business day for cards taken before 3 PM PT, or within 2 business days on standard deposits | Recorded as a separate fee withdrawal |
Stripe
Stripe pays out on a schedule you choose, and "each payout reflects your available account balance at the time it was created" (Stripe docs). So one payout holds every payment that became available, minus fees and any refunds or disputes. If refunds outrun sales, Stripe debits your bank instead. To see what's inside a payout, open it under Balances and then Payouts or download the payout reconciliation report.
Square
Square groups card sales by your close of day so that "a full day's business activity is included in one transfer" (Square support). Its processing fees "are deducted before funds are transferred to your linked bank account" (Square fees). Next-business-day transfers don't go out on Saturdays, so Friday's sales post by Monday morning.
QuickBooks Payments
Each day, QuickBooks Payments "combines all of your customer payments (both sales receipts and paid invoices) into a single record," which Intuit calls a deposit (Intuit). Because it's Intuit's own processor, QuickBooks Online records the batch and "a separate fee withdrawal" for you (Intuit). That's less work than a Stripe or Square batch. It's still one bank line for a day's invoices, with the fee as its own line to track.
If QuickBooks grouped a day's payments differently from your bank, Intuit's guide to fixing deposits shows how to regroup them.
For the fees themselves, see our guide to QuickBooks payment processing fees and how to avoid QuickBooks ACH fees.
Other reasons a deposit won't match an invoice
Batching is the usual cause, but it isn't the only one. If the numbers still don't line up, check these four.
- The customer paid part of the invoice. Enter the amount that arrived in the Amount received field. QuickBooks lowers the customer's balance by that amount and leaves the rest open.
- The payment went to the wrong account. If it was saved to another account, the bank line has nothing to match. Open the payment and check its Deposit to field.
- The payment was recorded twice. This happens when a payment applied to the invoice also gets added from the bank feed as new income. Intuit's fix is to undo the added deposit and match the bank line to the payment instead.
- The deposit was never made. Payments in Undeposited Funds stay there until you record a bank deposit, so the bank feed finds no match. Create a bank deposit, tick the payments it holds and check that the total equals the bank line.
When each one is the right pick
- You ring up dozens of small card sales a day. Batching is the right unit. Nobody matches a $14 ticket to a bank line, so you reconcile the day's sales summary to the day's deposit. Stripe, Square and QuickBooks Payments were built for that volume, and they handle it well.
- You send fewer, larger invoices. A $6,200 progress payment from a general contractor has to land on one specific invoice. So does a $4,800 payment from a distributor's customer. That's the business one-to-one settlement is for, and it's Nickel's default.
What Nickel does when a customer pays
We think a deposit should match the invoice it pays. When a customer pays a Nickel invoice by ACH or card, Nickel sends that payment to your bank on its own. That adds up to thousands of payouts a week, and each one carries a single customer payment. One-to-one is the default, not the only option. If your books run on daily batches, talk to our team about batching your deposits instead.
On the books, the QuickBooks Online integration records each payment in the bank account you mapped and applies it to its invoice. QuickBooks shows it as "Paid via Nickel" with the payment ID. When the deposit shows up in your bank feed for the same amount, QuickBooks pairs it with that payment and you confirm the match.
ACH is free on every plan, so an ACH deposit is the invoice amount to the cent. For cards, Nickel's default is to send the full payment and collect its 2.9% fee as a separate withdrawal. The deposit still equals the invoice, and the fee is one line to book to an expense account.
Not every line is an invoice. Refunds, ACH returns and chargebacks show up as their own lines, and so do transfers to or from Nickel Banking. The rule is one deposit per customer payment, not one invoice per bank line.
Nickel Bill Pay works the same way in the other direction. Each bill is one withdrawal for the bill amount, recorded against the bill in QuickBooks. Check and wire fees arrive as separate withdrawals, so your vendor receives the bill amount.
FAQs
Why is my Stripe deposit less than my invoice?
A Stripe payout is the net of everything in that batch. It holds the payments minus Stripe's fee on each one, and minus any refunds or disputes. To see the list, open Balances and then Payouts in the Stripe Dashboard. The payout reconciliation report shows the gross, fee and net amount for each transaction.
What is Undeposited Funds in QuickBooks Online?
It's a holding account, also called Payments to Deposit. When you record a payment, "the funds are added to this account" until you deposit them into your bank account (Intuit). Batch deposits run through it, because you group the day's payments into one deposit that equals the bank line. With Nickel, each payment is recorded to the bank account you mapped, so there's nothing to group.
How do I record a batched deposit in QuickBooks Online?
Record each customer payment to Undeposited Funds as it comes in. When the batch lands, check the processor's payout detail to see which payments it holds. Then create a bank deposit in QuickBooks that groups those payments. Add the fee as a negative line in an account such as Bank Charges & Fees, so the deposit total equals the bank line. Finally, match it in the bank feed. If that's a weekly chore, a sync tool can build the deposits for you, or a processor that settles one-to-one removes the step.
Does one-to-one settlement cost more?
With Nickel it costs nothing extra. ACH is $0 on every plan, including the free Core plan, and credit cards are 2.9% flat. The QuickBooks Online integration is free too. Stripe and Square charge extra for faster transfers, and those still come out of a pooled balance rather than one payment at a time.
Does every bank line match an invoice with Nickel?
No. Customer payments and bill payments each land as one line. Refunds, ACH returns and chargebacks land as their own lines too. So do card-fee withdrawals and Nickel Banking transfers. What you won't see is several invoices rolled into one deposit.
Can Nickel batch deposits instead?
Yes. Nickel settles one-to-one by default, and it can batch deposits for businesses that reconcile by the day. Talk to our team to set it up.
Does QuickBooks Payments batch deposits too?
Yes. Intuit's help center says QuickBooks Payments combines each day's customer payments into one record, which it calls a deposit. QuickBooks Online books the batch and the fee withdrawal for you, which is easier than reconciling a Stripe or Square batch by hand. The bank statement still shows one line for the day.
Every invoice deserves its own deposit
If your bookkeeping week starts with a payout report, send one invoice through Nickel and watch it land on its own. ACH is free, card fees are their own line, and the QuickBooks Online integration is included on the free plan. If you're still comparing options, we lined up the QuickBooks Payments alternatives.
Start for free, or talk to our team if you'd like a walkthrough first.
