Understanding Payroll Check Options in QuickBooks Online

Managing payroll is a critical task for any business, and payroll check in QuickBooks Online offers multiple options to streamline the process. Whether you're paying employees by direct deposit, printing checks, or recording manual payments, QuickBooks Online makes it simple—once you understand the tools at your disposal.

In this article, we’ll walk you through the different payroll check options in QuickBooks Online, how to use them, and tips to stay accurate and compliant.

Types of Payroll Checks in QuickBooks Online

1. Direct Deposit

Direct deposit is the most common method for paying employees through QuickBooks Online Payroll.

Key Features:

• Funds go directly to employees’ bank accounts

• Requires employee banking information

• Must submit payroll by a set cutoff time (usually 2 business days in advance)

Why Choose It:

• Secure and fast

• Reduces paper use and manual check handling

• Automates the entire payroll process

2. Printed Checks

If you prefer or need to print physical checks, QuickBooks Online has built-in tools for that too.

How It Works:

• Select the print option after running payroll

• Use Intuit-compatible check stock

• Align and print using the check printing tool

Why Choose It:

• Useful for contractors or temporary employees

• Handy when direct deposit isn’t available

• Offers a paper trail and immediate payment

3. Manual Checks

Manual checks refer to handwritten or pre-issued checks that you record in QuickBooks after issuing.

How to Record:

• Go to the Payroll section

• Select Create paycheck

• Choose “Paper check” and enter details

• Mark as “Already printed” or “Already issued”

Why Choose It:

• Useful in emergencies or corrections

• Allows flexibility when the payroll schedule changes

• Keeps your records complete, even if checks are written outside the system

Setting Up Payroll Checks in QuickBooks Online

To enable payroll check options, you must:

1. Activate QuickBooks Online Payroll (Core, Premium, or Elite)

2. Add employees or contractors with complete profiles

3. Choose your preferred payment method for each employee

4. For printed checks:

   • Set up check stock and printer alignment

   • Choose Check Style (Voucher, Standard, Wallet)

5. For direct deposit:

   • Enter bank details and verify funding source

Best Practices for Payroll Check Management

• Double-check employee info before issuing checks

• Reconcile payroll transactions with your bank regularly

• Avoid duplicate entries—record only checks actually issued

• Use payroll reports to stay compliant with taxes and deductions

• Secure printed checks to prevent fraud or loss

Tax and Compliance Considerations

QuickBooks Online automatically calculates and files payroll taxes (depending on your plan), but you are still responsible for:

• Approving payrolls on time

• Verifying tax filings and payments

• Staying updated on local, state, and federal regulations

Make sure you review tax settings before issuing any payroll checks to avoid under- or overpayments.

Also Read: QuickBooks Error 17337

Final Thoughts

Understanding your payroll check options in QuickBooks Online helps you stay flexible and in control of how you pay your team. Whether it's direct deposit for speed, printed checks for convenience, or manual entry for special situations, QuickBooks provides the tools to do it right.

Take time to explore each option and set up your payroll system to match your business needs. The result? Fewer errors, smoother operations, and happier employees.