You can run payroll and pay your employees through Direct Deposit (DD) in QuickBooks Desktop. Sign up and activate this feature in QuickBooks Desktop by following the steps provided below.

Direct Deposit signup requirements

  • Supported version of QuickBooks Desktop
  • Active QuickBooks Desktop Payroll subscription
  • Federal Employer Identification Number (EIN)
  • Internet access
  • Bank account that can handle Automated Clearing House (ACH) transactions within the United States

Note: Nominal per-transaction and per-payroll transmission fees may apply. Terms, conditions, pricing, features, service options, and support are subject to change without notice.

Sign up for Direct Deposit

  1. Go to the Employees menu, then select My Payroll Services > Activate Direct Deposit.
  2. Complete and review the form.
    1. In the Verify Your Company Information section:
      1. Select Edit.
      2. Make sure the Zip code has only 5 digits. Do not include the extension.
      3. From the Industry drop-down, choose the industry which closely reflects your company’s main business.
      4. Enter the owner's or principal's email address, 9-digit Social Security Number, and date of birth (mm/dd/yyyy). These are required according to the National Automated Clearing House Association (NACHA) rules and regulations.
      5. Edit the Payroll Administrator Information and confirm the email address.
    2. In the Enter Your Bank Information section:
      1. Enter the bank account information that Intuit QuickBooks Payroll debits for Direct Deposit transactions and fees. This is the bank account used to pay your employees.
      2. Select View Agreement, then read the document.
      3. Select the I have read and agree to the terms of service agreement checkbox.
      4. In the Check Security Limits section, answer the questions provided.
    3. Select Submit.

      Note: If nothing happens after selecting Submit, remove all the information on the form including the information on the Edit links. Manually re-enter the information, then select Submit again.

    4. A Confirmation page appears with the Next Steps instructions, which you can print.
    5. Select Return to QuickBooks at the bottom.

Before you use Direct Deposit…

  1. Verify your bank account.

    For security purposes, when you provide your initial bank information during signup, Intuit makes 2 small withdrawals of less than $1.00 each from the bank account you set up for Direct Deposit. These amounts are used to verify that you are the authorized user of the account and that the bank account is ready for authorized payroll transactions and fees. For more information, see Enter Direct Deposit test debits.

  2. Set up your employee's bank account information in QuickBooks.

    Collect bank account information from employees who want to be paid by Direct Deposit. Employees must give written approval to you for Direct Deposit of their paychecks. For more information, see Set up, edit, and remove Direct Deposit for Employees in QuickBooks Desktop.

  3. Create paychecks for Direct Deposit.

Direct Deposit processing timeline

  1. Direct Deposit is sent to Intuit BEFORE 5 pm PST, 2 banking days before the check date.

    Note: You can send paychecks up to 45 days in advance.

    • The transaction is still considered Pending.
    • You can void any previously sent paychecks or send additional paychecks.
    • The payroll offloads at 5 pm PST.
    • Holiday reminder.
  2. Payroll is offloaded AT 5 pm PST, 2 banking days before the check date.
    • The transaction can’t be stopped from being processed.
    • The payroll is electronically sent to the Automatic Clearing House (ACH) for processing.
  3. Intuit debits your bank account 1 banking day before check date.
    • This can happen within a 24-hour window.
    • The funds should be available in the bank account no later than 5 pm PST, 2 banking days before the check date.
    • If the payroll is returned due to NSF, you can check this article to know more.
  4. Funds are posted (pay day).
    • Funds are deposited to your employee’s account on the check date.
    • The Direct Deposit posting time or the availability of funds is determined by the employee’s bank and is not controlled by Intuit.
    • If the check date falls on a non-banking day, the funds are posted in the employee’s bank account on the next banking day.
    • The employee’s bank only has until 5 pm local time on the day of the check date to post the funds to the employee’s bank account.
    • To know more about when funds are posted, see When do direct deposits post?

    Late Direct Deposit checks

    If you send Direct Deposit checks later than 2 banking days before the check date, the employees you pay by Direct Deposit won’t receive their pay on the check date.

    You can set up a payroll schedule so QuickBooks can remind you when you need to create and send payroll.

    I get a Late Payroll warning while entering hours and reviewing paychecks.

    You can change the Direct Deposit checks to Printed checks. Either clear the Use Direct Deposit checkbox in the Preview Paycheck window or clear the check in the Direct Deposit column on the Review & Create Paychecks windows.

    I get a Late Payroll warning while attempting to send Direct Deposit paychecks to Intuit.

    Change the paycheck from Direct Deposit check to a Printed Ccheque. To do this:

    1. Go to the Pay Employees tab.
    2. Under Other Activities, select Edit/Void Paycheck.
    3. Select the appropriate check, then Edit.
    4. On the paycheck, select Paycheck Detail, then remove the check in the Use Direct Deposit checkbox.
    5. Select OK, then Save & Close. You can now print the paycheck with the rest of your payroll.


    Frequently Asked Questions

    How do I verify my bank account in QuickBooks Desktop?

    If you have the 2 small amounts from your bank, you can enter them in QuickBooks Desktop. Just go to the Employees menu > My Payroll Service > Activate Direct Deposit.

    How soon can I start using direct deposit?

    Immediately after verifying your bank account in QuickBooks Desktop, the Direct Deposit service is available to use. See Set up, edit, and remove Direct Deposit for employees in QuickBooks Desktop for more information.

    How do I process or send direct deposit in QuickBooks Desktop?

    Process payroll or create paychecks in QuickBooks Desktop the way you usually do, then send the Direct Deposit to Intuit.

    How soon can you deposit the funds to my employees' account?

    It takes 2 business banking days for Intuit to deposit the funds to your employees' bank accounts.

    Why is the Activate Direct Deposit option missing in my QuickBooks Desktop?

    This happens if the EIN in your QuickBooks Desktop company file has been previously signed up for Direct Deposit but was canceled. To reactivate:

    1. Go to the Employees menu, then select My Payroll Service > Account/Billing Information.
    2. Sign in using your Intuit Account credentials.
    3. On the Direct Deposit box, select Activate and follow the onscreen instructions.

If you get an error when performing these steps, reach out to our QuickBooks Desktop Payroll support for assistance.