In QuickBooks Desktop, open Edit › Preferences › Payroll & Employees to access payroll settings under Company Preferences.
Need to tweak paycheck defaults, show sick balances on pay stubs, or change mapping for wages and taxes? You’ll do it from the Payroll & Employees preferences inside the Desktop edition. This guide shows the exact clicks, what each area controls, and the little gotchas that waste time when you’re mid-pay run.
Find Payroll Preferences In Desktop Edition: Menu Path
The fastest route is the top menu. Sign in as QuickBooks Admin in single-user mode, then follow this path: Edit › Preferences › Payroll & Employees › Company Preferences. If you’re prompted to turn on Full Payroll, enable it, then return to the same tab. Intuit’s payroll preferences guide confirms this path and the features you’ll see on that screen, including Pay Stub & Voucher Printing and Sick & Vacation defaults.
What Lives Inside “Company Preferences”
That tab controls global behavior for paychecks and pay stubs. You’ll see checkboxes to recall hours between pay runs, toggle job costing and class tracking on paychecks, and buttons for Pay Stub & Voucher Printing and Sick & Vacation. These choices apply to everyone unless you override them on an employee record.
“My Preferences” Vs. “Company Preferences”
On the same Preferences panel there’s a personal tab. “My Preferences” changes how lists and windows behave for your user only—handy for display choices. The actual payroll behavior lives under “Company Preferences,” which affects the whole file.
Open Employee Defaults For Faster Setup
On the Payroll & Employees screen, select Employee Defaults. Here you can prefill a pay schedule, pay frequency, time data usage, and common tax settings. New hires then inherit those values. If you pay everyone weekly and most staff work in the same state, this one step trims setup time every season.
Set Sick And Vacation Accruals Once
Inside Sick & Vacation you can set how hours accrue, caps, and reset rules. Those defaults apply to new employees only. Existing profiles don’t change, which prevents accidental retro shifts in balances.
Show The Right Details On Pay Stubs
Select Pay Stub & Voucher Printing to choose what prints. Many states require showing sick or vacation balances, so flip those on if you’re subject to those rules. You can also mask all but the last four digits of SSNs and bank accounts.
Where To Edit Payroll Items, Accounts, And Mapping
Preferences control behavior, while the Payroll Item List controls content—wage types, deductions, company contributions, taxes, and additions you use on checks. Open it from Lists › Payroll Item List. Right-click any item to edit name, calculation method, linked expense or liability accounts, and default limits. If you need a different item type (say, a company contribution rather than an addition), create a new one and make the old one inactive—Desktop can’t convert an item’s type. This keeps history intact while you move forward with the right setup.
Update Where Costs Post In The Chart Of Accounts
If wage or tax amounts are landing in the wrong accounts, fix the mapping. Edit each affected payroll item and select the proper expense or liability account. For broad payroll accounting preferences tied to payroll, open Edit › Preferences › Payroll & Employees › Company Preferences and review the accounting section, then verify your chart of accounts. This keeps reports tidy and makes month-end close smoother.
Step-By-Step: Change Common Payroll Settings
Turn On Full Payroll Features
- Log in as Admin in single-user mode.
- Go to Edit › Preferences › Payroll & Employees.
- Open the Company Preferences tab.
- Select Full Payroll, then press OK.
Show Sick And Vacation Balances On Stubs
- Open Edit › Preferences › Payroll & Employees.
- Choose Pay Stub & Voucher Printing.
- Check the boxes for sick and vacation used/available.
- Save. Print a sample stub to confirm the layout.
Recall Hours Between Paychecks
- From Payroll & Employees › Company Preferences, find Recall quantity and hour fields.
- Leave checked if hours rarely change, or clear to prevent carryover.
Use Time Data To Build Checks
- On Employee Defaults, enable Use time data to create paychecks.
- Pick your time source (QuickBooks timesheets or QuickBooks Time).
Map Wages And Taxes To The Right Accounts
- Open Lists › Payroll Item List.
- Right-click a wage or tax item, choose Edit.
- Walk through the prompts until you reach the account mapping screen.
- Select the correct expense or liability account, then finish.
Pro Tips That Prevent Mid-Run Headaches
Use Single-User Mode For Preference Changes
Desktop locks some preference pages when multiple users are in the file. Switch to single-user mode before opening Payroll & Employees to avoid save errors.
Document Your Defaults
Snap a screenshot of Employee Defaults and Pay Stub & Voucher Printing. Save them in your accounting SOP folder. When staff changes happen, you won’t guess what the last admin checked.
Test With A Sample Paycheck
After changing preferences or item mapping, create one test paycheck in a sandbox copy or on a throwaway employee. Void it after review. That five-minute test catches missing accruals or wrong GL accounts.
Common Paths Inside Desktop Payroll
The table below lists the screens you’ll use most often and how to reach them from the top menu.
| Task | Menu Path | What You Can Change |
|---|---|---|
| Open global payroll preferences | Edit › Preferences › Payroll & Employees › Company Preferences | Stub content, sick/vacation defaults, recall hours, job costing/class. |
| Set Employee Defaults | Edit › Preferences › Payroll & Employees › Employee Defaults | Pay schedule, frequency, time import, common taxes. |
| Edit or create payroll items | Lists › Payroll Item List › Right-click item › Edit (or Payroll Item › New) | Names, calculation method, accounts, limits. (Item type cannot change.) |
Troubleshooting When Options Don’t Show
You Don’t See “Payroll & Employees” In Preferences
Payroll may be disabled in the file or your user lacks rights. Ask the Admin to enable payroll services and open the same Preferences panel while logged in as Admin. If you use Assisted Payroll, some controls are fixed to protect filings.
“Payroll Item List” Is Empty Or Hidden
Make sure you’re in the correct company file and that payroll is active. If items are missing, try toggling the filter at the footer of the list, then check whether you’re viewing another name list by mistake. Items tied to past transactions can’t be deleted, but you can rename or make them inactive.
Changes Didn’t Flow To Existing Employees
Employee Defaults affect only new profiles. To change current staff, open each employee in the Employee Center and update the required fields, or use an import tool if you have many records.
Amounts Hit The Wrong Accounts
That’s a mapping issue. Edit each affected payroll item and choose the proper expense or liability account, then rerun the report. For rare cases where you need separate accounts by group, duplicate the item and assign the new one to the right employees.
When To Use Payroll Center And When To Use Preferences
The Payroll Center is your daily hub: paying staff, paying liabilities, and filing forms. Preferences are the “rules” that shape those tasks. If stubs print missing balances, that’s a preferences fix. If a wage rate is wrong for one person, open that employee record instead. If a deduction posts to the wrong GL every time, edit the payroll item.
Quick Reference: Menu Paths You’ll Use Weekly
Preferences
- Edit › Preferences › Payroll & Employees › Company Preferences
- Edit › Preferences › Payroll & Employees › Employee Defaults
Payroll Items
- Lists › Payroll Item List › Edit
- Lists › Payroll Item List › Payroll Item › New
Time Tracking And Job Costing Settings That Affect Payroll
If you bill time to customers or track labor by project, open Edit › Preferences › Time & Expenses, set Do you track time? to Yes, and choose the first day of the work week. Back on Payroll & Employees, keep Job Costing, Class & Item tracking selected. That pairing feeds labor to job and class reports without manual entry.
Version Notes And Service Limits
Pro, Premier, and Enterprise share the same paths for the screens listed here. If you use Assisted Payroll, some options are controlled by Intuit to safeguard filings. You’ll still use the same Preferences panel for stubs, accrual defaults, and recall choices, while Assisted handles e-file setup and tax table updates.
Security, Review, And Audit Hygiene
Keep changes traceable. Before you modify defaults or mapping, make a backup (File › Back Up Company) with a clear name that includes the date. After edits, rerun Payroll Summary and Payroll Item Detail for the pay period you plan to process next. Save PDFs of those reports to your month-end folder so reviewers can see what changed and when.
Proof And Sources
The menu path and controls described above match Intuit’s official guide to Payroll & Employees preferences. It also explains the Pay Stub & Voucher Printing and Sick & Vacation defaults on that screen. For accounting mapping tied to wages and taxes, Intuit’s article on payroll accounting preferences outlines where to manage posting accounts and how QuickBooks records liabilities and expenses.