Conversion issues can occur after your conversion is complete. There are two common post-conversion issues that can happen:
- Customer balances are off in QuickBooks Online
- Invoices or sales transactions were converted to journal entries after importing to QuickBooks Online
How do I fix: Customer balances are off in QuickBooks Online
After conversion, you may notice that customer balances are off. This could likely happen if you used journal entries in QuickBooks Desktop to apply payments to your customer's invoices. The links between the journal entry "credits" and the invoices are broken once in QuickBooks Online. These discrepancies will not be noticed in the Profit and Loss or Balance Sheet report.
First, turn on Auto-apply credits in QuickBooks Online, then follow these steps:
Select the Gear icon on the Toolbar.
Under Your Company, select Account and Settings (or Company Settings).
- Select Advanced on the left.
- In the Automation section, mark Automatically apply credits box.
- Select Save.
How do I fix: Invoices or sales transactions were converted to journal entries after importing to QuickBooks Online

- This can happen if you have flat rates (0.00) for Sales Tax items or groups in your Desktop file.
- To keep your sales transactions from importing as journal entries, you'll need to edit the sales tax item "rates" category.
- Typically, this occurs in Mac files because in QuickBooks for Windows, you cannot save a sales tax item without a % symbol.
- If you have multiple items with flat sales tax rates in them, you'll have to edit all the item rates to ensure all your transactions import properly.
- Sales tax items being converted to journal entries with flat rates is an expected behavior because, at this time, those types of rates are not supported by QuickBooks Online.