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Get your Payroll questions answered by a QuickBooks Product Manager here -

What to do after converting from QuickBooks Desktop for Windows to QuickBooks Online

Here are some things you should do after converting your QuickBooks Desktop file to QuickBooks Online to ensure a smooth migration.

We highly suggest you keep your data file in QuickBooks Desktop and maintain your transactions on both sets of books until you determine QuickBooks Online is right for your business.

Verify and compare your financial reports

To make sure data was transferred successfully, compare the Profit and Loss and Balance Sheet standard reports in QuickBooks Online and Desktop.

Check the AR and Undeposited Funds account balances individually when comparing the reports. Learn what doesn’t come over from QuickBooks Desktop to Online.

When running your reports, make sure:

  • The date is set to "All Dates" in both products.
  • Your accounting method is set to accrual.

Expected report discrepancies:

  • Cash basis - Reports may not necessarily match using this accounting method. This is because QuickBooks Desktop and Online don't consider transactions as paid the same way.
  • Stock recalculation - Your reports may not match up if you imported your stock information due to FIFO recalculations that may have taken place. There'll be a task on your homepage that has a form which will need to be filed with the IRS stating the Stock Accounting changes that took place.
  • Multi-currency - Transactions with 3 different types of currencies involved do not convert to QuickBooks Online at this time.

Review your accounts' detail types

Is account detail type the same as sub-accounts?

After conversion, QuickBooks Online keeps your sub-account hierarchy. However, it also uses an additional level of account typing called "Detail Type." Detail types allow you to be more specific with your account organisation. For example, expense accounts can have a number of detail types, such as Advertising, Supplies and Materials, Legal Fees, and so on.

The conversion process assigns detail types to accounts where the detail is obvious (e.g. Undeposited Funds). For accounts where it isn’t clear what the detail type should be (a majority of accounts are like this), the conversion process assigns a generic detail type, such as Other Miscellaneous Income. You can correct this later.

Run the Account Listing Report to review and edit your accounts’ detail types.

  1. Select Reports from the left menu.
  2. Search for and open the "Account List" report.
  3. Review your accounts.
  4. To edit an account's detail type, select the account name.
  5. From the Detail Type drop-down, choose the correct detail type.
  6. Select Save and Close.

Complete your Payroll setup

If you imported Payroll data from QuickBooks Desktop for Windows

Transactions and payroll accounts are converted to balance your books, but details behind the transactions (like payroll item breakdowns and employee year-to-date numbers) don't convert.

Liability refunds, adjustment transactions, and opening balance transactions that affect accounts convert to journal entries.

To complete your payroll setup:

  1. Select Employees from the left menu.
  2. In the "Paid in [Year]" column, be sure each employee who received a payroll payment this year is switched to Yes.
    Note: Employees who haven't been paid in the current year will automatically be listed as No.
  3. To enter and/or verify your year-to-date payroll totals and employee info, select Complete payroll setup.
  4. To complete the setup, follow the onscreen instructions.
  5. Use "Run Payroll" once you're ready to pay your employees.

Additional steps

  • If you were using E-services to pay/file your taxes electronically, you'll need to re-enroll for this service in QuickBooks Online. Just log in, then, go to Gear icon and select Payroll Settings.
  • If you were using or want to use Direct Deposit for your employees, you'll need to add your employer and employee's individual bank account info. This can be done from the "Payroll Settings" page, or from the "Employee Setup" screen.
  • Finally, you'll need to enter/reconcile any historical tax payments you made so far this year.
    Select Employees from the left menu, then Payroll Tax. From here, select Enter prior tax history and begin to add all of the past tax payments that you made for various agencies so far this year. They should balance out against your liabilities (excluding any current unpaid tax liabilities) so far this year.

Regarding pay history and certain pay types:

  • When supported, your payroll history (the setup screen) will come over. You'll only need to verify the totals. If your payroll history doesn't convert, we'll guide you on how to enter these year-to-date totals to get going again.
  • If you reported "Group Term Life Insurance" or "S-Corp Owners Health Insurance", our system will recalculate net pay per the calculations for QuickBooks Online Payroll. Keep this in mind when comparing your QuickBooks Online Payroll Summary reports to your QuickBooks Desktop Summary reports.

QuickBooks Merchant Services are currently not supported in QuickBooks Online. You can either e-invoice your customers with PayPal or GoCardless, or find a suitable app.

Get to know FIFO (if you imported stock)

Once imported to QuickBooks Online, the calculation method for your stock will be FIFO (first-in-first-out), using the "as of" date that you chose during import.

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