Check Run: How to Run AP Check Payments, and How to Shrink Them
A check run is the batch in which accounts payable selects approved, due invoices and prints or issues checks to pay them, usually on a fixed weekly or biweekly schedule. It's how most companies still pay the vendors that haven't moved to electronic payments.
For many AP teams, it's also the slowest and riskiest hour of the week. Two people tied up for half a morning, a signer who has to be found, a stack of paper that carries the company's bank account number, and then a few days in the mail. A clean check run makes that hour safer. A good AP strategy makes it shorter every quarter.
Key Takeaways
A check run batches approved, due invoices into one printing and signing cycle. A payment run does the same thing across every payment method, including ACH and card.
A sound check run follows a fixed sequence, from selecting invoices and reviewing exceptions through signing, positive pay, mailing, and reconciliation.
Checks remain the payment method most exposed to fraud, so segregation of duties, signature thresholds, and a positive pay file before release belong in every run.
The real cost of a check run is the staff time and fraud exposure. The paper and postage are the small part.
Shrinking the run means triaging vendors, moving the ones who accept cards or ACH, and accepting that a few will keep demanding checks.
What is a check run in accounts payable?
A check run in accounts payable is a scheduled batch of check payments. AP pulls every approved invoice that's due before the next run, generates the checks in one pass, gets them signed, and mails them, instead of cutting checks one at a time as invoices come in.
Batching exists for control and efficiency. One run means one approval point, one signing session, one positive pay file sent to the bank, and one set of postings to the ledger. ERPs are built around it. Sage Intacct's help documentation, for example, describes using a check run "to process up to 1,000 checks at a time in an offline process." Other systems set their own limits, but the idea is the same everywhere. The check run sits at the end of the accounts payable process, after invoices have been received, matched, and approved.
How often do companies do check runs?
Most companies do check runs weekly or every two weeks. The cadence follows cash planning and payment terms, since a team paying on net 30 terms can batch weekly without paying anyone late.
Smaller companies sometimes run monthly, and heavy-volume companies may run twice a week. The right frequency is the slowest one that still pays every invoice on time and captures any early-payment discounts worth taking. Running more often than that adds signing sessions without adding much value, while running less often pushes invoices past their due dates.
What's the difference between a check run and a payment run?
A check run batches check payments only. A payment run batches every payment due in the cycle, whether it goes out by check, ACH, or virtual card.
The distinction matters more as fewer vendors take checks. Many companies still call the weekly cycle "the check run" long after half of it has moved to ACH. Treating it as a payment run, with one selection and approval step that then splits by payment method, keeps the electronic payments under the same controls as the paper ones. It also makes the remaining checks visible as exceptions rather than as the default.
How do you process a check run, step by step?
A check run follows the same sequence every cycle. Each step should have a named owner and should leave a record that an auditor can follow.
Select due invoices. AP runs a report of approved invoices due before the next run, including any with early-payment discounts.
Review exceptions. AP removes invoices on hold, disputed, or missing a receipt, and checks for duplicates.
Approve the batch. A manager or controller approves the payment proposal, with totals by vendor.
Print or transmit. AP prints checks on secured stock or sends the file to an outsourced print service.
Sign. Authorized signers sign manually or apply a controlled electronic signature, following signature thresholds.
Send the positive pay file. Treasury sends the bank a list of check numbers, amounts, and payees before any check is released.
Mail. Checks go out with remittance detail, and the mailing date is logged.
Post and reconcile. Payments post to the ERP, and cleared checks are reconciled against the bank statement.
A missed step usually shows up later somewhere else. Skip step 2 and you find the duplicate on a vendor statement. Skip step 6 and the bank has nothing to compare a forged check against.
How do you pick which invoices go in the run?
Pick invoices by due date first, then by discount opportunity, and then remove anything on hold. The goal is to pay everything that will be due before the next run, and nothing earlier unless a discount pays for the early cash.
Holds deserve their own look each cycle. Invoices held for a pricing dispute, a missing receipt, or a vendor bank-detail question tend to sit quietly until the vendor calls. A weekly glance at the hold list during selection keeps those from aging into late payments. Invoices that haven't completed the invoice approval workflow shouldn't make it into the run at all, however urgent the vendor sounds.
Who should approve and sign the checks?
Someone outside AP should approve the batch, and a separate authorized signer, or two above a set threshold, should sign the checks. The person who prepares the run shouldn't approve or sign it.
Signature thresholds matter more than most teams admit. I've seen a Friday run slip to Tuesday because every check over a low threshold needed a second signature and the second signer was on a plane. What fixed it was a written threshold set high enough that routine payments need one signature, with the second signer reserved for the large or unusual ones. A faster printer would have changed nothing.
What controls belong in an AP check run?
Every AP check run needs controls that separate who prepares, approves, signs, and reconciles, plus a positive pay file sent to the bank before any check leaves the building. Checks are still the payment method criminals target most.
According to AFP's 2026 Payments Fraud and Control Survey, 76% of U.S. organizations experienced attempted or actual payments fraud in 2025, and 58% reported that checks were subject to fraud. A working control set includes:
Segregation of duties between invoice entry, run approval, check signing, and bank reconciliation, following the principles of segregation of duties in AP
Written signature thresholds, with dual signatures above a set amount
Locked custody of blank check stock, with a log of check numbers used
A positive pay file sent to the bank before release
A void and reissue log, so every replaced check is accounted for
Independent verification of any change to vendor bank or address details
Those controls only hold up if someone can prove they ran. An AP audit trail that records who selected, approved, signed, and released each batch is what an auditor will ask for first. Every vendor moved off paper removes that exposure, and Corpay pays suppliers by virtual card, ACH, or check from one approval flow.
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How does positive pay protect a check run?
Positive pay protects a check run by letting the bank compare every presented check against the list the company sent. If the check number, amount, or payee doesn't match, the bank flags it for the company to approve or reject.
That turns the bank into a second line of defense. A thief who washes a stolen check and changes the payee name still has to get past a file that says who the check was written to. Positive pay works only if the file goes to the bank before the checks are mailed, which is why it sits ahead of mailing in the procedure.
What are the warning signs of check fraud?
The warning signs of check fraud include checks clearing for amounts or payees that don't match the run, checks presented far from the vendor's location, and vendors calling about payments the bank shows as cashed.
Mail theft has made these more common. FinCEN's 2023 alert on mail theft-related check fraud reported that check-fraud suspicious activity reports passed 680,000 in 2022, nearly double the prior year. Watch, too, for the fraud that follows vendors off paper. A request to switch a vendor from checks to ACH is exactly the moment criminals impersonate that vendor, and business email compromise caused $3,046,598,558 in reported losses in 2025, according to the FBI's 2025 Internet Crime Report. Verify every bank-detail change by calling a number already on file. The rise of check fraud is a good reason to move vendors electronic, but only with that verification in place.
What does a check run really cost?
A check run costs far more than paper and postage. According to AFP's 2022 Payments Cost Benchmarking Survey, issuing a paper check costs a median $2 to $4, against $0.26 to $0.50 for an ACH payment. That's 2022 data, and the gap has probably widened since.
Even that understates it, because the survey figure covers processing and leaves out several costs:
AP hours spent selecting, printing, and chasing signers
Calls from vendors asking where their check is
Stale checks that never get cashed and have to be voided and tracked
Fraud losses from a single altered check
My view is that the cost of a check run lives in the people and the exposure. Check stock is the cheapest part of it, and a business case built on postage savings leaves most of the argument on the table. Working out the true cost of paper checks for your own volume is worth doing before the next budget cycle.
The strongest outside signal comes from the federal government. Executive Order 14247, issued by the White House in March 2025, ordered Treasury to stop issuing paper checks effective September 30, 2025. The order says paper-based infrastructure cost taxpayers over $657 million in fiscal 2024 and that Treasury checks are 16 times more likely than electronic transfers to be lost, stolen, undeliverable, or altered. When the largest payer in the country decides the era of government paper checks is over, the case for a corporate AP team to keep printing them gets hard to make.
How do you move vendors out of the check run?
Move vendors out of the check run by sorting them into groups, then working each group toward the cheapest electronic method it will accept. Most vendors can move. A few can't, and planning for that up front keeps the effort honest.
The trend is already running in your favor. Commercial checks collected through the Federal Reserve fell to 2,796 million in 2025, down 6.1% from 2024 and from 16,994 million in 2000, according to the Federal Reserve's commercial check collection data, which counts Fed-cleared checks only. ACH is absorbing the difference. Nacha's study of B2B check payments over 21 years found B2B ACH volume rose 155% from 2015 to 2024, from 2.9 billion to 7.4 billion payments, and Nacha's report on ACH Network volume in 2025 counted about 8.1 billion B2B payments in 2025, up about 10%.
Vendor group | What to offer | What it takes |
Already accepts cards | Virtual card | A short enrollment call and remittance setup |
Takes ACH but not cards | ACH | Verified bank details, confirmed by phone |
High volume, check by habit | ACH or card, with faster payment | Outreach to the vendor's AR team |
Requires checks by policy | Check, through an outsourced print service | Positive pay and tight address controls |
Occasional or one-time | Whatever the vendor already accepts | Usually not worth enrollment effort |
Enrollment is the real work. Someone has to call each vendor's receivables team, explain the payment timing, collect and verify details, and follow up on the first payment. That outreach is where most check-reduction efforts stall. Corpay's fully managed AP handles that vendor outreach as part of the service, and most clients are live in weeks.
Which vendors should move to virtual cards first?
Move high-volume vendors that already accept cards first. They need the least persuasion, and every invoice they're paid by card leaves the check run permanently.
A single-use virtual card issued for one invoice also removes the fraud problem a check creates, since the card number is good only for that amount and that vendor. Card payments earn rebates, too, which helps fund the enrollment effort.
What about vendors who refuse anything but checks?
Some vendors will refuse anything but checks, and that's fine. Keep them in a smaller, tightly controlled run, ideally printed and mailed by an outsourced service with positive pay in place.
Ask again once a year, since policies change when a vendor's own bank or ERP changes. If a vendor prefers ACH but has never been asked, offering an ACH payment with earlier settlement is often enough. What you're aiming for is a check run so small that it stops being a weekly event.
Let Corpay run your payment run
The check run eats a morning every week, creates the company's highest fraud exposure, and depends on finding a signer. Most of that work doesn't have to sit with your AP team.
With Corpay's fully managed AP, you approve one payment file and Corpay pays each vendor the way it accepts payment, by virtual card, ACH, or check, including printing and mailing the checks that remain. Corpay handles vendor enrollment and follow-up, so vendors move out of the check run without your team making the calls. Card payments use single-use virtual cards and earn rebates, with Corpay paying its customers more than $800M in rebates each year. Corpay AP automation connects through 100+ ERP integrations, including NetSuite, Sage Intacct, Business Central, and Acumatica, and AP teams save about 40% of the time they spend on processing. Most customers are live in weeks.
Frequently Asked Questions
What is a check run?
A check run is a scheduled batch in which accounts payable pays approved, due invoices by check. AP selects the invoices, gets the batch approved, prints and signs the checks, sends a positive pay file to the bank, mails the checks, and posts the payments to the ledger.
What is a cheque run?
A cheque run is the same thing as a check run, spelled the British and Canadian way. It's the regular batch in which a company prints, signs, and sends cheques to pay approved supplier invoices.
How often should AP do a check run?
Most AP teams run checks weekly or every two weeks. Choose the least frequent schedule that still pays every invoice by its due date and captures worthwhile early-payment discounts, since each extra run adds another round of approvals and signatures.
What controls should a check run have?
A check run should keep preparation, approval, signing, and reconciliation with different people. It also needs written signature thresholds, locked check stock, and a positive pay file sent before release, plus phone verification of any vendor bank-detail change.
How do you reduce the number of checks you write?
Sort vendors by what they'll accept, then move high-volume card-accepting vendors to virtual cards and the rest to ACH. Verify every new bank detail by phone, keep a small controlled run for vendors who insist on checks, and ask those vendors again each year.
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