How to Print Payroll Checks in QuickBooks Online

Payroll checks in QuickBooks Online do not print the way vendor checks do. If you have run payroll and then gone looking for those paychecks in your usual print queue, they are not there, and nothing is broken. This guide walks the actual path, the setup that has to happen first, and the one design decision that catches almost everyone out.

Quick Answer

To print payroll checks in QuickBooks Online, first set your printing preference under Settings, then Payroll Settings, then the Printing section. Choose paycheck on check paper, pick one or two pay stubs, and run the alignment. Then go to Payroll, Employees, Paycheck list, and print from the Action column.

Quick Summary

• Payroll checks print from Paycheck list, not from the + New, Print checks queue. They will never appear there, and that is by design.
• Set the print preference first under Settings, Payroll Settings, Printing, or you will print stubs on plain paper by mistake.
• Payroll has its own alignment setting, separate from vendor checks. That is why the same stock can print correctly for one and wrong for the other.
• Alignment uses a letter and number grid: letters move the print up and down, numbers move it left and right.
• Choosing paycheck and 2 pay stubs requires a voucher check with two stubs. Standard three per page stock will not work.
• Reprinting uses the same path as printing. Filter the paycheck list by date or employee to find the one you need.

Here is the whole process at a glance.

If you still need stock that matches, our QuickBooks checks are formatted to the standard layouts and ship fast.

What this guide covers

• Why don't my payroll checks show up in the Print checks list?
• How do you set up payroll check printing in QuickBooks Online?
• Which check stock do you need before you print?
• How do you fix payroll check alignment?
• How do you actually print the paychecks?
• How do you print stubs for direct deposit employees?
• How do you reprint a paycheck you already printed?
• What goes wrong most often?
• Getting your next payroll run right
• Frequently Asked Questions

Why don't my payroll checks show up in the Print checks list?

QuickBooks Online keeps payroll check printing separate from regular check printing, so paychecks never appear in the + New, Print checks queue. Print them from the Paycheck list under Payroll instead.

This is the question that sends most people searching, so it belongs first.

The separation is built in. When you run payroll, the paychecks post to your bank register, but they do not get tagged for the standard print queue. Open + New and then Print checks, and they are simply not listed.

That is deliberate. Payroll checks carry earnings and deduction detail that the regular check print flow is not built to render, so they route through the Payroll module instead.

What this means in practice:

• You cannot batch payroll checks together with vendor checks in one print run
• You cannot fix the problem by editing the paycheck and ticking a print later box
• You must print paychecks from the Paycheck list inside Payroll

Our separate guide to printing checks in QuickBooks Online covers the vendor and expense side, which is the flow that does use the print queue. The two processes look similar and share almost nothing.

How do you set up payroll check printing in QuickBooks Online?

Setup happens once, in Payroll Settings, and it decides what comes out of the printer later. Skip it and QuickBooks Online will use whatever it was last set to, which for most new accounts means pay stubs on plain paper.

The path:

1. Select Settings, the gear icon
2. Select Payroll Settings
3. Find the Printing section and select Edit
4. Choose your output: pay stubs on plain paper, or paycheck on QuickBooks-compatible check paper
5. If you chose check paper, select Print paycheck and 1 pay stub or Print paycheck and 2 pay stubs
6. Select Align check and work through the alignment
7. Select Save, then Done

Where do I find this if my account says QuickBooks Workforce?

Same place. Intuit rebranded its payroll products as QuickBooks Workforce, so your account may show Workforce Payroll, Premium or Elite rather than the old Payroll Core, Premium or Elite. The printing settings sit under Payroll Settings either way.

What is the difference between 1 pay stub and 2 pay stubs?

This choice determines which physical check stock you need, which is why it matters more than it looks.

The two stub option is the common choice for payroll, because one stub goes to the employee and one stays in your records. It needs a check on top voucher format. If you try to run it on three per page stock, there is nowhere for the stub detail to land.

Which check stock do you need before you print?

Settings only work if the paper matches them. Payroll is the format-sensitive case, because the stub has to carry earnings and deduction detail that a vendor check never needs.

If you are ordering for payroll specifically, payroll business checks come in the voucher format, and QuickBooks checks on top match the voucher style QuickBooks expects. For a wider comparison, see types of business checks.

Before you buy, our QuickBooks check compatibility guide covers what makes a check work with QuickBooks, and check position guide explains how to confirm the layout your setup expects.

How do you fix payroll check alignment?

Payroll alignment is configured inside Payroll Settings, and this is the detail that trips up experienced users: it is a separate setting from your regular check alignment.

That is why the same box of checks can print perfectly for vendor payments and land a few millimeters off for payroll. Two settings, two results, one box of paper.

To fix it:

1. Go to Settings, then Payroll Settings
2. In the Printing section select Edit
3. Choose Paycheck on QuickBooks-compatible check paper
4. Select Align check, then Print alignment form
5. Compare the printed sample and enter the letter and number combination that fits best
6. Select Save, then Done

What do the letters and numbers mean?

The alignment form uses a grid. Letters run A to X and control vertical position. Numbers run 0 to 9 and control horizontal position.

Two habits that save paper:

• Test on plain paper first. Print the alignment form on ordinary paper, then hold it against a real check up to a window. You will see instantly whether the fields land in their boxes.
• Record the combination you settled on. Write it on the box. If someone resets the setting or you change printers, you are not starting over.

How do you actually print the paychecks?

Once setup is done, printing is short. Paychecks live in the Paycheck list inside the Payroll module.

1. Go to Payroll, then Employees
2. Select Paycheck list, which sits below Run payroll
3. Use Filter to narrow by Date range or Employee if you have a long list
4. In the Action column, select the print option
5. Review the preview window, then select the printer icon

Load your check stock before you hit print, and load it in the orientation your test run confirmed. Voucher checks are directional, and a reversed stack wastes the whole run.

Should you print one at a time or in a batch?

For a handful of employees, printing from the list one at a time is fine and gives you a chance to catch a jam before it eats the stack. For larger runs, filter the list to the pay period first so you are not scrolling past old paychecks.

Either way, count the printed checks against the payroll register before you distribute them. Our guide to making payroll checks covers the wider run process, including recording and distribution.

How do you print stubs for direct deposit employees?

If you pay by direct deposit, you do not need check stock at all. Set the printing preference to pay stubs on plain paper, and the same Paycheck list prints a stub with no check attached.

The path is the same one you already use:

1. Go to Settings, then Payroll Settings, then Printing, then Edit
2. Choose pay stubs on plain paper
3. Save, then print from Payroll, Employees, Paycheck list as usual

Two things worth knowing if you run a mixed payroll:

• The setting is account wide, not per employee. If some staff take paper checks and others take direct deposit, you will be switching the preference between runs or printing in two passes.
• Stub delivery may already be handled. Employees with online access can usually retrieve their own stubs, so printing is for your records or for staff who want paper.

How do you reprint a paycheck you already printed?

Reprinting uses exactly the same path as printing. There is no separate reprint screen.

1. Go to Payroll, then Employees
2. Open Paycheck list
3. Use Filter to set the Date range or pick the Employee
4. Find the paycheck and print it from the Action column

One practical warning. A reprint produces another physical check carrying the same check number unless you change it.

If the first copy was damaged and destroyed, that is fine. If it already left the building, you now have two checks in circulation under one number. That is a reconciliation problem and a fraud risk.

Void the original properly before reprinting a check that is already out.

What goes wrong most often?

Five recurring issues, and what actually fixes each one.

The pattern across all five is the same: payroll printing has its own settings, its own screen and its own stock requirement. Most problems come from applying vendor check knowledge to a payroll run.

Why do my paychecks print in reverse order?

Reverse order is a printer setting, not a QuickBooks one. If the last employee comes out on top of the stack, the printer driver is set to output pages last to first.

Open your printer preferences and look for a page order or paper handling option, then switch it from reverse to normal. It is worth fixing before a large run, because a reversed stack has to be re-sorted by hand against the payroll register.

What if you are not using QuickBooks Online Payroll at all?

Plenty of small employers calculate payroll elsewhere, or by hand, and just need the checks. That works, and the printing path is different because there are no paychecks in the Payroll module to print.

In that case you are writing or printing checks through the normal check flow, or by hand from a manual book. Our guides to payroll checks and manual business checks cover what the stub has to contain either way, and can payroll checks bounce covers the account side.

Getting your next payroll run right

Three things to take away.

Payroll checks print from the Paycheck list, never from the regular print queue. If you remember one thing, make it that one, because it is the source of most of the confusion.

Your printing preference and your check stock have to agree. Choosing two pay stubs and loading three per page stock will not work, no matter how carefully you align it.

And payroll alignment is its own setting. If vendor checks print cleanly and payroll does not, you have found the reason.

If you need stock that matches your setup, payroll business checks and QuickBooks checks ship fast, and computer checks covers the full range of positions. If you are not sure which format your setup expects, get in touch and we will work through it with you. First time ordering? Start with ordering business checks for the first time.

About the Author

Written by the Checks Next Day content team. We print and ship business and payroll checks for US businesses every working day, which means format questions, stub requirements and alignment problems come to us constantly. This guide reflects what payroll customers ask most often. It is general information rather than accounting or tax advice, so confirm your own payroll obligations with your accountant.