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Setup export of IOP data to QuickBooks Online (QBO)

SOLVEDby QuickBooksIntuit Online Payroll11Updated April 20, 2021


This article provides detailed instructions on how to export to QuickBooks Online and what to do each time you run payroll.

Expected Outcome

You can export payroll data to QuickBooks Online.


You have completed Intuit Online Payroll setup and are setting up export to QuickBooks Online.
  • Exporting to QuickBooks Online Accountant is not currently supported because QBOA already includes a payroll subscription
  • You are using a supported and up-to-date browser.


  1. Set up your QuickBooks Online accounts for payroll data

    If you have not yet set up payroll accounts in QuickBooks, Intuit will set them up for you the first time you import data into QuickBooks. Just enter the account names you prefer at the Export Preferences page following the instructions in Step 4.
    If your QuickBooks company already contains appropriate accounts, you can choose the accounts directly from your QuickBooks Chart of Accounts. If you need to add an account (perhaps for a new deduction), type the name you want for the account in our payroll service and they will be set up the account in your QuickBooks company the first time you transfer data.
    If you have not set up employees in QuickBooks they will be entered the first time you transfer data. If you have already set up employees in QuickBooks, ensure the name in QuickBooks is the exact same names in the Online Payroll employee setup. Note that we export employee names with a period after any middle initial, for example: John M. Smith.
    • To check the list of accounts in QuickBooks Online, select Reports, then in the Search bar, type Account List and select this report. Find the name of the bank account you use to write payroll checks and the expense accounts for employee wages and employer payroll taxes. Find the liability accounts you use for tax and deduction liabilities. (For cash advance and loan repayment, use asset accounts.)
    • If you use subcategories or subaccounts, use a colon to separate the category name from the subcategory; for example: Payroll:Gross Wages (no space before or after the colon)
  2. Set up QuickBooks classes

    If you have not yet set up classes that apply to your employees in QuickBooks, create them now. Once the classes have been set up, write down their names or print the list of classes and highlight the ones you will use for the payroll data.
  3. Set up connection to QuickBooks Online

    We have updated the export setup flow between IOP and QBO.
    1. In our payroll service, select the Setup tab.
    2. Under the Export heading, select Preferences.
    3. Select QuickBooks Online from the software drop down list.
    4. We will search for any existing QBO accounts under the current the current user ID.
    5. First, we search for an existing QBO account attached to the current user ID.
    6. If we don't find one, you will be asked to login to your Intuit Account.
    7. Since QBO only accounts don't require security questions, the system may prompt the customer to select a security question and answer.
    8. If the correct account is found, you can continue to the export process. If multiple accounts are found, you will be prompted to select one.
    9. Next, we will complete the connection process.
    10. Once completed, you can complete the export settings. NOTE: Select Payroll Liability accounts and Payroll Expense accounts to prevent any errors when setting up or exporting your payroll data.
    11. You are also given the option to change the QBO company you sync with.
  4. Set up accounts in your Intuit Online Payroll account.

    You will use the Export Preferences page to enter your QuickBooks accounts. Use the exact same names of the QuickBooks accounts you will use for the payroll data.
    1. In the Checking Account box, enter the name of the bank account or select from the drop-down list. This is the account from which you write paychecks.
    2. Select Customize to enter the account names exactly as they appear in QuickBooks or select from the drop-down list.
      • When entering accounts, read the help topics next to each field to choose the right account type. In general, enter or select an expense account for the Wage and Tax Categories. For the Liability accounts, enter or select the corresponding QuickBooks Liability account. NOTE: In QuickBooks, the detail type of the liability account must be Payroll Tax Payable in order to prevent any issues with setting up or exporting your payroll data.
      • If using a cash advance or employee loan deduction, enter or select an asset account to receive the payroll data.
      • If you use different accounts for different groups of employees, select that option in the wage/tax category section to enter or select different QuickBooks accounts for each employee.
      • If you use different accounts for different types of wages/taxes, select that option in the wage/tax category section to enter or select different QuickBooks accounts for each pay type and tax type.
    3. Specify whether you use QuickBooks classes. These classes must be set up already in QuickBooks.
    4. If classes are selected, you will enter them on the next page after clicking OK at the bottom of this page.
    5. If you want to print checks using QuickBooks, select I will print paychecks using QuickBooks. Note: If you select this option, see pay split between paper check and direct deposit below.
    6. Select OK.

  5. What to do after you create paychecks or tax payments

    1. Create paychecks or tax payments as usual.
    2. Approve your checks or payments.
    3. From the Pay Day tab, select Export.
    4. Select the checks and payments you want to export.
      • If you're exporting for the first time, checks and payments from the last six months should already be selected.
      • If you don't see your checks, change the date range.
    5. Select Export.
    6. We begin transferring the payroll data to QuickBooks.
    7. When you see the Congratulations message, close the window.
    8. Verify that all transactions appear in your QuickBooks register.
      Note: Because of the complexity of moving transactions from one web site to another, it's important to verify that all transactions have been transferred. If any transaction does not appear in your QuickBooks register after a few minutes, transfer it individually. (Go to the Pay Day tab, select Export, then select Show Checks and Payments Already Exported. Update the date range to include paychecks to transfer, select the paychecks, then select Export.)

What happens when your data is entered into QuickBooks

When your payroll data is transferred to QuickBooks, the process creates one transaction in your bank account register for each payroll service paycheck. Depending upon how you set your preferences, handwritten checks appear in the checking register with or without check numbers. If you set your preferences to mark paychecks to print in QuickBooks, the transactions will not have check numbers but will be marked to print. (Transactions for direct deposit are also included in the checking account register but have no check numbers and are not marked to print.)
The Bank account transaction contains splits that affect multiple accounts, depending on the number of accounts you selected to receive deductions:
  • A split appears for the Wage Account you specified in the export preferences.
  • A split appears for the Tax Account you specified in the export preferences.
  • One or more splits appear for each Liability account for federal, state and local taxes owed.
  • Additional splits are entered for each deduction/garnishment, one for the employee's deduction and one for any company contribution.
When tax payments are exported, they are recorded in the corresponding QuickBooks tax liability account and reduce the liability.
These transactions in QuickBooks accounts keep your balance sheet and profit and loss statements up to date. Remember that you should continue to do all of your payroll reporting using our payroll service.

Pay split between paper check and direct deposit

We recommend that you print checks in our payroll service, not in QuickBooks. If you choose to print checks from QuickBooks, only the paychecks can be printed from QuickBooks. The pay stubs will still need to be printed from Online Payroll.
Currently, you must NOT print a paper check in QuickBooks for a paycheck created with our payroll if your employee receives part of their pay as a direct deposit and part as a paper check. If you print a check in QuickBooks for this type of a pay transaction, the printed check will include the amount already direct deposited and you will overpay the employee.

Disconnecting and reconnecting to another QuickBooks Online company

If you export payroll to more than one QuickBooks Online company, you must disconnect from one company before exporting to another.
In QuickBooks Online, to disconnect:
  1. Select My Account
  2. Select Connection List.
    • For newer QuickBooks Online accounts, paste the following URL into your browser and then press Enter: https://qbo.intuit.com/app/sdkapplist
  3. Select Online Payroll: Intuit Online Payroll Service.
  4. Select Delete.


In Online Payroll, to reconnect and export:

  1. At the Preferences page, select Export Preferences,
  2. Select QuickBooks Online from the program list.
  3. At the page that appears for transferring, select CONNECT.
  4. Follow the instructions on the page to connect your payroll account to the other QuickBooks Online Edition company.

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