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How to Set Up Payroll Direct Deposit in QuickBooks Online

Direct deposit is a convenient feature in QuickBooks Online that allows you to pay employees directly into their bank accounts. Setting it up ensures your payroll process is smooth and efficient, saving you time and eliminating the need for paper checks. Here's a step-by-step guide to help you set up payroll direct deposit in QuickBooks Online.

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Step 1: Ensure You Have QuickBooks Payroll

Before setting up direct deposit, make sure you’re subscribed to one of QuickBooks’ Payroll plans. Direct deposit is included in these plans, so if you’re not already signed up, consider upgrading your QuickBooks Online account to include payroll services.


Step 2: Gather Required Information

To set up direct deposit, you’ll need:

  • Your business’s bank account information (including routing and account numbers).

  • Employee banking details (routing and account numbers).

  • Employer Identification Number (EIN).

  • A voided check or bank verification letter for your business account.


Step 3: Activate Direct Deposit

  1. Log into QuickBooks Online and navigate to the Payroll menu.

  2. Select Employees, then choose an employee to set up direct deposit for.

  3. Click Edit or Add direct deposit info under the employee’s payment details.

  4. Enter the employee’s bank account type, routing number, and account number. Verify the information is correct.

  5. Click Save to update the employee’s payment information.


Step 4: Set Up Your Business Bank Account

  1. Go to the Settings menu and select Payroll Settings.

  2. In the "Bank Accounts" section, click Edit or Add Bank Account.

  3. Enter your business bank account details, including routing and account numbers.

  4. QuickBooks will perform a verification process:

    • Instant Verification: Log in to your bank account through QuickBooks for immediate setup.

    • Manual Verification: QuickBooks will deposit two small test transactions into your account. Check your bank statement in 2-3 business days, then enter the exact deposit amounts in QuickBooks to complete verification.


Step 5: Verify Direct Deposit Information

Once both your business and employee bank accounts are set up, review all information to ensure accuracy. Incorrect details can delay payroll processing or result in failed payments.


Step 6: Process a Payroll Run

After setting up direct deposit:

  1. Go to the Payroll menu and click Run Payroll.

  2. Enter employee hours or salary details and confirm the pay date.

  3. Review the payroll summary to ensure all payments are correct.

  4. Submit the payroll at least two business days before the pay date to ensure timely deposits.


Tips for Smooth Payroll Direct Deposit

  • Check Deadlines: Submit payroll by 5 PM PST two business days before payday for timely processing.

  • Communicate with Employees: Inform employees when their first direct deposit will occur.

  • Secure Information: Always handle banking details securely to protect sensitive information.

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Troubleshooting Common Issues

  • Failed Deposits: Double-check employee and business bank details for accuracy.

  • Verification Delays: Ensure your bank account is eligible for ACH transfers and follow up with QuickBooks support if test deposits don’t appear.

  • Employee Questions: Provide employees with clear instructions on how direct deposit works and when to expect their payments.


By following these steps, you can set up payroll direct deposit in QuickBooks Online quickly and efficiently. It’s a great way to streamline payroll and provide a seamless payment experience for your employees. If you encounter any issues, contact QuickBooks Support at 1-877-593-7885 for assistance.

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