# How to Run Payroll in QuickBooks Online and QuickBooks Desktop?
**Running payroll** doesn’t have to be stressful. Whether you use QuickBooks Online Payroll or QuickBooks Desktop Payroll, you can pay employees accurately, stay compliant, and keep records clean with a clear, repeatable process. This in-depth guide walks you through scheduled and unscheduled payroll, direct deposit and paper checks, and the best practices that keep your team paid on time, every time.

## Why Choose QuickBooks for Payroll?

QuickBooks payroll tools are built to simplify one of the most important business tasks: paying your people. With built-in tax calculations, flexible pay schedules, and tight integration with accounting, you can:

* Run payroll faster with fewer errors
* Pay by direct deposit or paper check
* Track wages, taxes, and benefits in one place
* Generate and distribute pay stubs easily
* Keep employee records and reports organized

If you’re on QuickBooks Online Core, Premium, or Elite Payroll, you can pay both employees and contractors. Desktop users get powerful, local control with reliable paycheck processing and reporting.

## Before You Run QuickBooks Payroll: Essential Setup Checklist

No matter which version you use, a quick setup check saves time and prevents mistakes:

* Confirm your payroll service (Online vs. Desktop).
* **Complete Payroll Setup:** company details, tax agencies, pay schedules, and benefits.
* **Review Employee Profiles:** pay rates, tax forms, direct deposit info, and deductions.
* Verify bank accounts for payroll tracking and funding.
* Sync time tracking if you use QuickBooks Time or timesheets.

Once these are in place, running payroll becomes a smooth, repeatable routine.


## How to Run Payroll in QuickBooks Online Payroll?

QuickBooks Online Payroll lets you process both scheduled and unscheduled payroll. Scheduled runs handle regular paychecks, while unscheduled runs cover bonuses, commissions, or special payments.

### A. Scheduled Payroll (Regular Paychecks)

Use scheduled payroll for your normal pay cycle—weekly, biweekly, semi-monthly, or monthly.

1. Open **Payroll** from your apps and go to **Employees**.
2. Select **Run payroll** and choose the **correct pay schedule**.
3. Review the **pay period and pay date**.
4. Select the **employees** you want to pay.
5. Edit each paycheck if needed:
* Enter hours, overtime, or salary details
* Add bonuses, reimbursements, or memos
* Review approved time if you use QuickBooks Time
6. Click **Preview payroll** to double-check totals and taxes.
7. Choose the bank account to track payroll.
8. Review details and **Submit** payroll.

After submission, QuickBooks schedules direct deposits for the chosen pay date and prepares pay stubs for distribution.

### B. Unscheduled Payroll (Bonuses, Commissions, or One-Off Payments)

Unscheduled payroll is perfect for special situations like bonuses, commissions, fringe benefits, or final checks.

1. Go to **Payroll > Employees** and open the **Run payroll** dropdown.
2. Choose Bonus only, Commission only, or Fringe benefits only.
3. Answer any prompts about taxes or calculations.
4. Confirm the pay period (if applicable) and pay date.
5. Select the employees and edit paycheck details as needed.
6. Preview payroll to confirm accuracy.
7. Select your **payroll bank account**.
8. Either **Save** for later or **Submit** payroll.

Once submitted, QuickBooks processes payments and generates pay stubs you can share with your team.

## What Happens After You Submit in QuickBooks Online?

* Direct deposits process on the scheduled pay date
* Pay stubs become available for employees
* Payroll records update automatically in your books
* Taxes and withholdings track correctly for reports and filings

**Next Steps:** Print or email pay stubs, review payroll reports, and make sure your tax settings stay current.

## How to Run Payroll in QuickBooks Desktop Payroll?

QuickBooks Desktop Payroll focuses on reliable paycheck processing, especially for businesses that prefer paper checks or local control. You can run scheduled payroll, unscheduled payroll, or a termination check.

### A. Payroll Types Explained

* **Scheduled Payroll:** Your regular pay cycle
* **Unscheduled Payroll:** Off-cycle payments like bonuses or corrections
* **Termination Check:** Final paycheck for a departing employee

### B. Step-by-Step: Running Payroll in QuickBooks Desktop

1. Open **Employees** and select **Pay Employees**.
2. Choose the **payroll type**:
* Scheduled Payroll
* Unscheduled Payroll
* Termination Check
3. If scheduled, pick the correct schedule and click **Start Scheduled Payroll**.
4. Confirm key details:
* Pay period end date
* Check date
* Bank account
5. Select the **employees** you want to pay.
6. Enter hours worked:
* Type them directly into the grid, or
* Pull them in automatically from timesheets
7. Open **Paycheck Detail** to review earnings, taxes, and deductions.
8. Click **Save & Next** to move through employees or Save & Close to return.
9. Select **Continue**, review printing or direct deposit options, and confirm amounts.
10. Click **Create Paychecks** to finalize.

### C. After You Process Payroll in Desktop

* Paychecks and pay stubs are ready to print or distribute
* Payroll data updates in your company file
* You can reprint checks or stubs anytime
* Reports reflect wages, taxes, and deductions accurately

## QuickBooks Online vs. Desktop Payroll: Which Is Right for You?

QuickBooks Online Payroll works best if you want cloud access, easy direct deposits, and automatic updates. It’s ideal for teams that need flexibility and remote access.

QuickBooks Desktop Payroll fits businesses that prefer a local setup, paper checks, or tighter control over in-house processes.

Both options deliver accurate calculations, strong reporting, and dependable payroll workflows the right choice depends on how you run your business.

## Pro Tips for Faster, Error-Free Payroll

* Lock in your pay schedules and stick to them to avoid last-minute rushes.
* Review employee profiles monthly to catch tax or rate changes early.
* Use time tracking integrations to reduce manual entry.
* Always preview payroll before submitting—this step prevents costly mistakes.
* Keep reports organized for audits, budgeting, and year-end filings.

## Final Thoughts

**Running payroll in QuickBooks** doesn’t need to feel complicated. With the right setup and a clear process, you can pay employees on time, stay compliant, and keep your books clean whether you use QuickBooks Online Payroll or QuickBooks Desktop Payroll. Follow the steps above, build a routine, and payroll day will become just another smooth part of running your business.

## Frequently Asked Questions
### Q. Can QuickBooks Online Payroll integrate with QuickBooks Desktop?

QuickBooks Online Payroll does not directly integrate with QuickBooks Desktop. Each platform uses its own payroll system. If you use QuickBooks Desktop, you’ll need QuickBooks Desktop Payroll instead. However, you can still export reports or move your accounting data to QuickBooks Online if you decide to switch platforms in the future.

### Q. Is payroll support still available in QuickBooks Desktop?

Yes, payroll support is still available for QuickBooks Desktop, as long as you have an active QuickBooks Desktop Payroll subscription. You can run payroll, create paychecks, calculate taxes, and generate payroll reports. Keep in mind that support and features depend on your specific Desktop version and subscription status.

### Q. What steps fix QuickBooks when it won’t let me process payroll?

If QuickBooks won’t let you process payroll, try these steps:

1. Make sure your payroll subscription is active
2. Update QuickBooks to the latest version
3. Download the latest payroll tax table
4. Check your system date and time settings
5. Verify your company file for data issues
6. Restart QuickBooks and your computer

If the problem continues, running the QuickBooks Tool Hub or contacting QuickBooks support usually resolves deeper issues.

### Q. Why can’t I run payroll in QuickBooks after updating the software?

This usually happens because the update didn’t fully install or your payroll tax table didn’t update correctly. Common fixes include:

* Restarting QuickBooks and your computer
* Updating the payroll tax table manually
* Checking your subscription status
* Running QuickBooks as an administrator
* Repairing or re-installing the update if needed

Once everything is synced properly, payroll should run normally again.

### Q. How do I enable payroll services in QuickBooks Desktop?

To enable payroll in QuickBooks Desktop:

1. Go to **Employees** in the **top menu**
2. Select **My Payroll Service > Activate Service**
3. Sign in with your **Intuit account**
4. Follow the **on-screen steps** to link your subscription
5. Download the **latest payroll updates**

After activation, you can start setting up employees and running payroll.

### Q. How do I process payroll using the QuickBooks mobile app?

In QuickBooks Online, you can run payroll from the mobile app with these steps:

1. Open the **QuickBooks app** and **sign in**
2. Tap **Payroll**
3. Select **Run Payroll**
4. Review employee hours and pay details
5. Confirm **taxes and totals**
6. **Submit payroll**

This is great for quick payroll runs, approvals, or last-minute checks when you’re away from your desk.

### Q. What’s the process to issue a bonus payroll in QuickBooks Online?

To run a bonus payroll in QuickBooks Online:

1. Go to **Payroll** and select **Employees**
2. Click **Run Payroll** and choose **Bonus only**
3. Select the employees receiving the bonus
4. Enter the **bonus amounts**
5. Review tax settings (bonuses are usually taxed differently)
6. Preview payroll and **Submit**

QuickBooks will calculate the taxes and generate pay stubs automatically.

### Q. In what situations should I use the Auto Payroll feature in QuickBooks Online Payroll?

Auto Payroll is best when:

* Your employees are salaried and paid the same amount every cycle
* Your payroll is consistent and predictable
* You want to save time and avoid manual runs
* You rarely change hours, pay rates, or deductions

It’s not ideal if your team has variable hours, frequent bonuses, or changing pay. In those cases, manual payroll gives you more control.