How to print checks in QuickBooks Online and Desktop: set up voucher or standard stock, fix check alignment, and find checks missing from the print queue.
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Last updated August 2026.
To print checks in QuickBooks Online, open the check and select Print later so the check number changes to To print, then go to Expenses & Bills > Expense transactions > Print checks, choose the bank account the money leaves, enter the starting check number and select Preview and print. QuickBooks Desktop does the same job from File > Print Forms > Checks. The first run through, both versions walk you into a setup screen that asks whether you use voucher or standard stock and then lets you nudge the printing until it lands on your pre-printed checks.
Two things cause most of the support tickets. The print queue is filtered by bank account, so a check you wrote thirty seconds ago can look like it vanished purely because a different account is selected at the top of the Print checks screen. And QuickBooks Online does not print the MICR line along the bottom edge of a check, which means blank paper will not work: the stock has to arrive already encoded for your bank.
Everything below covers QuickBooks Online and QuickBooks Desktop side by side, including the alignment screens in each, the check stock that actually feeds correctly, what to do when a run jams halfway, and how a check you printed gets matched once it finally clears the bank.
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Mark the check Print later, open Expenses & Bills > Expense transactions > Print checks, select the bank account the money comes out of, tick only the checks you want in this run, type the number printed on the first sheet in the tray, then select Preview and print.
Open the check and select Print check instead of Print later. QuickBooks takes you straight to the preview for that single check, assigns the next number in sequence, and skips the batch screen entirely. It is the right choice for a one off payment you are handing over today.
Use the queue instead when you cut checks in weekly runs. Batching keeps the numbering continuous, keeps the stock loaded once, and gives you a single confirmation step at the end rather than a decision per check.
Standard checks fit three to a page with no stub. Voucher checks put one check at the top and two detachable stubs underneath, printed with the invoice or payroll detail behind the payment. QuickBooks asks which one you use during print setup and lays the page out differently for each, so picking the wrong style is itself an alignment problem.
| Check style | Checks per page | What the stub shows | Best for |
|---|---|---|---|
| Standard | Three | Nothing. There is no stub | High volume vendor runs where remittance detail is emailed separately |
| Voucher | One | Two copies of the payment detail: bills paid, invoice numbers, or payroll breakdown | Payroll, and vendors who need to see exactly which invoices a payment covers |
| Wallet | Three, narrower, with a side stub | A short side stub for a manual note | Small businesses writing occasional checks by hand |
Voucher stock costs more per check but it removes an entire category of vendor email, because the remittance advice is physically attached to the payment. If you pay bills in batches, the stub is what tells the vendor which of their invoices the single grouped payment covered.
From Print checks, select Print setup, choose voucher or standard, then print the sample QuickBooks offers and hold it against a real check. If it does not line up, select No, continue setup. You have to select that twice before the fine tune alignment screen appears, which is why so many people never find it.
Print the sample on plain paper, not on real stock. Lay the plain sheet on top of a blank check and hold both up to a window or a lamp. The printed fields should sit inside their boxes with a comfortable margin. Do this once, properly, and you will not touch the setting again unless you change printers or buy stock from a different supplier.
Open Print checks > Print setup > No, continue setup twice to reach Fine tune alignment. QuickBooks shows an alignment grid in a preview window and a large square representing the page. Drag the grid inside the square to wherever it actually landed on your printed sample. The horizontal and vertical numbers below the square change as you drag.
Those two numbers are offsets in the same units as the grid, and they are the only thing QuickBooks stores. If your sample printed too low, drag the grid down to match, and QuickBooks will compensate by printing higher. Work in small steps and reprint a plain paper sample after each change. Two or three passes normally gets it, and the setting sticks per company file.
Almost always one of four things: the wrong check style selected in print setup, the browser scaling the PDF to fit the page, paper guides that let the stock drift in the tray, or an alignment offset that was never set at all. Rule the printer out before you touch the QuickBooks offsets.
| What you see | Usual cause | Fix |
|---|---|---|
| Everything is shifted uniformly down or across | No alignment offset saved | Run Fine tune alignment and drag the grid to match your sample |
| Fields are close but slightly compressed or stretched | The print dialog is scaling the page | Set scale to 100 percent or Actual size, never Fit to page |
| First check is right, third check drifts up the page | Cumulative scaling across a three up sheet | Print from Adobe Reader at Actual size rather than the browser viewer |
| Alignment changes run to run | Stock shifting in the tray | Tighten the paper guides and load a smaller stack |
| The amount prints in the payee area | Wrong check style chosen in setup | Reopen Print setup and switch between voucher and standard |
| The memo line prints too low | Printer specific top margin | Adjust the vertical offset only, in small increments |
The scaling one catches people repeatedly. QuickBooks Online hands the browser a PDF, and browser print dialogs love to default to a fit to page setting that shrinks everything by a couple of percent. On a single check that is invisible. Spread across three checks on one sheet it compounds, which is exactly why the bottom check on the page is the one that ends up wrong. Downloading the PDF and printing it from Adobe Reader at Actual size removes the variable entirely and needs far fewer adjustments.
Write or queue the check with Print Later ticked, then go to File > Print Forms > Checks. Choose the bank account, confirm the first check number, select the checks to include and print. Desktop then asks whether the batch printed correctly, the same way QuickBooks Online does.
Desktop keeps its printer configuration separately under File > Printer Setup, where you pick the form name (Check/PayCheck), the printer, the check style and the printer type. Set the printer type to Page-oriented for a normal laser or inkjet, and Continuous only if you genuinely run a tractor feed printer. Getting that dropdown wrong makes every later alignment attempt behave strangely.
Go to File > Printer Setup, choose Check/PayCheck in the Form Name list, then select Align. Desktop offers a coarse adjustment and a fine adjustment. Coarse is only available for continuous feed printers and Intuit supplied forms, so on a standard laser printer with third party stock you go straight to fine.
Fine alignment prints a sample with a small grid on it, and you type in the vertical and horizontal offsets based on where the sample landed. If you print partial pages, the Partial Page tab is separate: it asks how your printer feeds a short sheet, centered, portrait or landscape, and it has its own alignment. A batch that lines up perfectly on a full sheet and fails on the last two checks of a page is nearly always a partial page setting, not a main alignment problem.
Check the Account dropdown at the top of the Print checks screen first. The queue only shows checks drawn on the account currently selected, so a payment made from a second bank account is invisible until you switch to it. That single dropdown explains most missing check reports.
If the account is right, open the transaction itself and confirm Print later is actually ticked. A bill paid through a scheduled online payment never enters the paper queue at all, because QuickBooks is sending the money rather than handing you a check to mail. And a payment that was saved with a real check number typed into the number field is recorded as a handwritten check, which deliberately keeps it out of the print list.
Not on its own. QuickBooks Online does not print the MICR line, the magnetic routing and account digits along the bottom edge, and it does not print your bank details or logo either. It fills in payee, date, amount, memo and check number onto stock that already carries everything else. Blank paper out of a normal printer will be rejected by the bank.
Printing on blank stock is possible, but it takes a dedicated MICR add on such as PrintBoss, MultiCHAX or VersaCheck plus certified MICR toner in a laser printer. That route makes sense if you write checks on many bank accounts and do not want to store pre-printed stock for each one. For a single operating account, pre-printed stock is cheaper and involves no extra software to maintain.
Buy stock sold as QuickBooks compatible in either voucher or standard layout, pre-printed with your company name and address, your bank name, and the routing and account numbers in MICR toner. Confirm the layout matches what you select in print setup, because the two styles put the payee and amount fields in different places.
Two practical notes. Order a small quantity from any new supplier first and run a plain paper sample against it, since a two millimetre difference in where a vendor prints the field boxes means redoing your alignment. And keep the stock locked up, sequential and logged: pre-printed checks are negotiable instruments the moment they are signed, and your auditor will ask how the sequence is controlled.
Type it into the Starting check no. field on the Print checks screen, matching whatever is physically printed on the top sheet in your tray. QuickBooks numbers the rest of the batch upward from there and writes those numbers into the register. It does not read the stock, so this field is the only thing keeping paper and books in sync.
If you tore off a check for a manual payment, or a previous run jammed and burned a sheet, the number in the tray no longer follows the last one QuickBooks used. Correct the field before you print, not after. Fixing a whole batch of wrong check numbers afterwards means editing each transaction one at a time, and every one of them will fail to match cleanly in the bank feed until you do.
Yes, and the confirmation screen after printing is where you say so. QuickBooks asks whether the batch printed correctly and offers three answers: all printed correctly, some need reprinting, or keep all checks in the print list. Only the checks you confirm as good leave the queue.
Answer accurately even when a run half fails. If you confirm everything printed and one sheet actually jammed, that check is marked printed with a number that only exists on a piece of ruined paper, and the queue will not offer it again. Choosing Some checks need reprinting puts the bad ones back so you can run them on fresh stock with corrected numbers. Void the ruined check in the register rather than deleting it, so the number stays accounted for in the sequence.
Open the transaction, untick Print later, type the real check number into the number field, and save. The check leaves the queue and is recorded as a handwritten check. Simply unticking it in the batch list only skips it for this run, and it reappears next time.
That distinction matters when you are cleaning up an old queue. A list of stale To print entries usually means checks that were hand written months ago and never reconciled against the queue. Give each one its real number rather than deleting the transaction, because deleting removes the expense from your books entirely.
It arrives as a separate transaction days or weeks later, when the payee actually deposits it. QuickBooks tries to match the cleared item to the check already sitting in your register, mostly on amount and date, and the check number in the bank description is what makes that match reliable rather than a guess.
This is where the numbering discipline pays off. If the batch printed with numbers that do not match the paper, the bank feed will offer to create a brand new expense instead of matching, and you end up with the same payment recorded twice: once when you printed it, once when it cleared. Outstanding checks that never clear are the other half of the problem, and they are what makes a reconciliation refuse to balance.
The practical requirement is simply having the bank data in QuickBooks to match against. If your bank does not offer a live feed for that account, or the connection keeps dropping, converting the PDF statement into a Web Connect .qbo file and importing it gives you exactly the same For review list, with the check numbers intact in the description field. Upload a statement at the top of this page and look at the parsed rows before you commit to anything.
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