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Set up direct deposit

Learn how to set up direct deposit in QuickBooks Desktop Payroll.

Do you want to sign up for direct deposit? It's easy in QuickBooks Desktop Payroll. We explain the requirements and show you how.

Signup requirements

Before signing up for direct deposit in QuickBooks desktop you need confirm the following.

  •  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, select My Payroll Services, then Activate Direct Deposit.
  2. Complete and review the form. In the Verify Your Company Information section:
    • Select Edit.
    • Make sure the Zip code has only 5 digits. Do not include the extension.
    • From the Industry drop-down, choose the industry which closely reflects your company’s main business.
    • 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.
    • Edit the Payroll Administrator Information and confirm the email address.
    • 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.
  3. Select View Agreement. Once looked over, 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.
  5. Select Submit. (If nothing happens after selecting Submit, remove all the information on the form. This includes information from the Edit links. Manually re-enter the information, then select Submit again.)
  6. A Confirmation page appears with the Next Steps instructions, which you can print.
  7. Select Return to QuickBooks at the bottom.

Before you use Direct Deposit

Once you sign up, but before you can use direct deposit, do the following three things.

  1. Verify your bank account.

    When you provide your initial bank information during signup, Intuit makes 2 small withdrawals of less than $1.00 each. These amounts are used to verify that you're the authorized user and the 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. (See this article for instructions:       Create paychecks for Direct Deposit.

Direct Deposit processing timeline

It's important to understand payment processing timelines, so deposits to your employees aren't delayed.

  1. Direct Deposit is sent to Intuit before 5 pm PST, two banking days before the check date. (Note: You can send paychecks up to 45 days in advance.) At this time: 
    • The transaction is still considered Pending.
    • You can void any previously sent paychecks or send additional paychecks.
  2. Payroll is then offloaded at 5 pm PST, two 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, two 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, your employees won’t receive their paychecks on time. (You can set up a payroll schedule so QuickBooks can remind you when you need to create and send payroll.)

If you're getting the following late alerts try the following:

 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.

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

Change the paycheck from Direct Deposit check to a Printed check.

  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

If you have the 2 small transactions, less than $1.00, from your bank, enter them in QuickBooks Desktop. Just go to the Employees menu, then My Payroll Service, then Activate Direct Deposit.

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

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

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, then 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.

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