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How to Set up Direct Deposit for Employees in QuickBooks

Last modified on July 26th, 2022 at 9:55 am

With direct deposit feature in QuickBooks Payroll, you can easily create & send a paycheck within the same company file. You could face data loss of the company file while sending paychecks.

What is Direct Deposit in QuickBooks Employee

QuickBooks Payroll makes it easy to deposit your employees’ wages. You can do so in their money market, savings, or checking accounts. You can send your employees their wages easily by wiring them to their bank account. There are benefits for both the employee and employer for using Direct Deposit.

The direct deposit is used in a number of scenarios, including the following:

1. Employee Pay:

Employers often use direct deposit for their employees. This lowers the costs for the company and gives employees a more convenient way to get paid.

2. Tax Refunds:

The United States prefers to send their citizens a tax refund using direct deposit. It is both secure and easy for the taxpayer. If you owe them a tax return, then simply set up to make it happen.

3. Stimulus Checks:

In 2020, the U.S. government will distribute the emergency assistance stimulus checks. The citizens who opted in the IRS direct deposit program will receive the checks in their bank account on their tax return.

How does Direct Deposit work?

The employer transfers paycheck using the direct deposit information of employees. The funds get transferred within 2 working days into the employer’s account. This digital fund transfer is easy and benefits both parties.

What are the Benefits of Setting Up Direct Deposit for Employees?

You can set up direct deposit for your employees by first doing the set up of payroll for direct deposits, then getting the authorization form and adding the direct deposit for your employees. The process is easy!

Step 1: Set up your company’s Payroll and Direct Deposit.

Here is the step-by-step process for setting up your company payroll.

  • First, find out what information you need. Learn about the bank, officer, and business.
    • Business name, address of business, and EIN.
    • Principal Officer social security number, home address, and date of birth.
    • Bank account numbers and bank credentials.
  • You need to connect with your bank account
    • Open QuickBooks software in your system.
    • Users can sign in using their credentials (User ID and password).
    • Go t the Employee menu.
    • In addition, select the My Payroll Service option.
    • Then click on the Activate Direct Deposit to start receiving your paycheck.
    • Select the button below to get started. If this is not visible then:
      • Click on I’m Admin and I’m the primary person who can do this. Enter the admin’s email address and User ID.
      • Click on Continue to proceed.
      • Sign in to your Intuit account and then log in.
      • Then click on Get Started.
  • Under the Business tab, click on Start. In the window that appears, mention all the information.
  • To continue, please enter all the required information
  • Now, mention the information of Principle officer and click the Next button.
  • The add new bank account.
  • Provide your bank’s name and if it asked for account number then provide it.
  • You have to create the pin for your account. You have to enter this pin in order to send payments or payroll. It’s a good idea to double-check your PIN.
  • Then click on the Submit button.
  • Then click the Next button then click the Accept and Submit.
  • When asked to please submit their social security number.
  • You see a message on your screen, like the below one:
    • Thank you for signing up for the QuickBooks Direct Deposit. Next is to activate your Direct Deposit via the last step, which requires you to verify your bank account.
    • Now, you can use your bank account to quickly pay your employees.
  • Verify your bank account into QuickBooks.
    • You need to check your banking account by 2 working days of the debit amount less than one dollar in QuickBooks Payroll.
    • When you are able to see how much you earned.
    • Start the QuickBooks software, enter an administrator password if necessary, and then log in to the program.
    • Click on the Employees tab.
    • My Payroll Service is beneficial.
    • After that, click on Switch to direct deposit.
    • Now, sign in to your Intuit account using your credentials (user ID and password).
    • Click on Reference twice, followed by Verify.
    • Enter the code that you created before.
    • Click the Submit button, then click the OK button.
  • You have to set up the bank information of your employees so they can direct deposit their paychecks. Follow step 4 that has detailed instructions.
  • Pay for your Employees Paychecks with Direct Deposit Intuit make it easy to manage. You create the paychecks and the company deposits them directly into their account so that they are sure to get their money on time.

Step 2: Receive a Direct Deposit Authorization Form.

Get the authorization to deposit your employees’ wages, and get a voided check from their bank account. These are for your records only and you don’t have to submit them into QuickBooks.

Step 3: Direct Deposit of Set-up of an Employee

The following steps works for Both QuickBooks Payroll 2020 and Intuit QuickBooks 2019 Payroll , So check your version first

  • Select Employees and then select the Employee Centre and then click on the Employee list.
  • Now, select the Employee’s Name
  • Then, select the Payroll Info Tab.
  • Now, select Direct Deposit button.
  • Then open Direct Deposit Window and then select Employee’s Name in the Direct Deposit
  • Now, check requirement (if you want to open paycheck with one account or more than one)
  • Enter details of the employee of your company (Name, bank name, account no., account type and routing no.)
  • For two accounts in paycheck deposit, enter the amount and the percentage that you want to deposit in the first account. The second will automatically get the remaining percentage.
  • Then select OK. The information will automatically save.
  • Then enter the direct deposit pin

The next paycheck that is created for employees will automatically be marked direct deposit. Delete and recreate the paycheck that has been created buy has not yet been sent. For a wrong bank account in direct deposit, you can use direct deposit to spot, open and remove the paycheck from it. QuickBooks MAC Payroll user might seen some different option on their screen .

Next to the direct deposit, you will see the checkmark box. Add information and select the direct deposit. For the service that has already been sent, you can’t add the direct deposit again for the same.

Step 4: Edit, Modify, Cancel Direct Deposit QB

You can easily update the employee’s direct deposit information on the same page.

You need to enter the Direct Deposit Pin here, enter the pin

  • Create the employee’s paycheck by editing back account information
  • For the older paychecks (created by account information update), the settlement would automatically be deposited and reflected in the older bank account.
  • However, in general sense, you need to avoid this. First of all, delete paycheck, recreate it and then send paycheck to QuickBooks.

There is one more way to do the same:

  • Open paycheck and then visit paycheck screen
  • Now, go to your paycheck details, de-select direct deposit option and then select Save → Save & Close.
  • Once again open paycheck and then click on the direct deposit button. Make sure that you save it properly.

Employee’s Profit Shouldn’t be Reflected with the Direct Deposit

Employees get many benefits with direct deposit, such as:

Simplified Budgeting:

Direct deposit is a good way to increase savings and spending. When the direct deposit is started, then you can request some amount of your paycheck to be deposited directly into your checking account.

No Need of Paperwork:

With direct deposit you can stop doing your paperwork. Every electronic payment that comes in is automatically recorded digitally so you don’t have to do the paperwork yourself.


Banks are now required by law to make it possible to direct deposit your paycheck. A system of protection is available to reduce fraudulent activity, while still giving you a convenient payroll solution.


There is no paper in the process. Everything can be done digitally, which means it is paperless. It’s a great choice to switch to direct deposit.

Help For QuickBooks Desktop Direct Deposit Issues

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