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Troubleshooting Your QuickBooks Integration

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Updated at Aug 08, 2025
By Kali Patrick

Table of Contents

Initial Set Up of QuickBooks Online General Things to Note Sync Times on Heavy Invoicing Days Tax Rate Inheritance Differences Between Syncro vs. QuickBooks Tax Rates Invoice Amounts Stale Object Errors (Force Update) Business Validation Error Wrong Customers Mapped / Issues Mapping Customers Failed Invoice Or Payment Failed Sync Wrong Person Displays on Invoice / Invoice Won't Sync

Related Docs

  • QuickBooks API Errors
  • Set Up QuickBooks Online (QBO)

In addition to the QuickBooks API Errors page, this document describes common issues with QuickBooks integrations so you can solve them quickly.

Note: Any error messages you see in Syncro regarding the QuickBooks integration comes directly from QuickBooks.

Initial Set Up of QuickBooks Online

If the authorization does not work during your attempt to Set Up QuickBooks Online (QBO), please contact Intuit to fix your Intuit ID. 

If payments do not sync after entering your account, the account name is probably incorrect. Revisit step 4 of the QuickBooks Settings Wizard, or change it using the QuickBooks Settings page.

If your purchase orders aren’t syncing, the AP Account name is probably incorrect. Revisit step 5 of the QuickBooks Settings Wizard, or change it using the QuickBooks Settings page.

Additionally, when a Purchase Order (PO) syncs with QuickBooks, you must create the bill and pay it in QuickBooks to receive the items in your inventory. Then you can return and receive the items inside Syncro. If you receive the items in Syncro first, it will close out the PO, so you’ll need to re-open it again to bill it. It is easy to miss a closed PO, so be sure to bill it and receive it in QuickBooks before closing it in Syncro to avoid discrepancies in your AP account and inventory. 

General Things to Note

Sync Times on Heavy Invoicing Days

The last day of the month and the first of the month are heavy invoicing days for QuickBooks. Because of this, invoices generated on those days of the month can take a full day to sync over.

Tax Rate Inheritance

Tax rates on line items in Syncro will override all other tax rates unless the customer is tax exempt. If a line item has not been assigned a specific tax rate, it will inherit the tax rate from the invoice.

Differences Between Syncro vs. QuickBooks

Tax Rates

If automatic sales tax calculations are enabled in your QuickBooks Online account, you may see a difference in tax amounts between Syncro and QuickBooks Online. Syncro is still sending over the amount calculated based on the tax rate added in Syncro, however, that rate is being overridden by the automatic tax calculation in QuickBooks Online. This is a setting on the QuickBooks Online end that is often set up when a new QuickBooks account is created.

Our team is aware of the inconvenience this causes, as the invoice has to be manually edited in QuickBooks Online to correct the tax. We are investigating potential solutions. In the meantime, to prevent needing to manually edit QuickBooks Online invoices, we ask that you reach out to Intuit to disable the automatic sales tax calculation feature so that Syncro tax rates are preserved in QuickBooks Online.

See also: Map Tax Rates.

Invoice Amounts

This happens because QuickBooks rounds to the nearest penny for every line item and then calculates the total, while Syncro calculates the full total of every line item, adds them all up, and then rounds the total at the very end. This often results in a $.01 -  $.02 difference in the total sum on invoices. To fix this, QuickBooks may automatically adjust your invoice by $.01. Otherwise, you'll need to manually adjust the invoice in QuickBooks. 

Stale Object Errors (Force Update)

Stale object errors are generated in QuickBooks and appear in Syncro when the systems detect there is a difference between an invoice in QuickBooks and Syncro. To fix this, you click Force Update in the error box to push the data from Syncro to QuickBooks. This button is not only safe to push, but we encourage pushing the data from Syncro to QuickBooks to ensure both invoices match.

Business Validation Error

If you see the QuickBooks error: “A business validation error has occurred while processing your request: Business Validation Error: Tax Exemption Reason should be specified in case customer is marked as not taxable,” edit the Organization's settings. 

Mark them as tax exempt, and select an exemption reason from the QuickBooks Tax Exempt Reason dropdown:

If you do not see this field, reach out to Support.

Note: The exemption reasons listed are those created by QuickBooks and cannot be updated in Syncro.

Wrong Customers Mapped / Issues Mapping Customers

QuickBooks Online uses the First Name, Last Name, Business name, Email address, and address fields both to map customers to the proper profile and to map invoices to the proper customer. For your invoices to match to the correct customers when they sync to QuickBooks, all of these fields should be unique, especially customer email addresses. If multiple customers in Syncro and/or QuickBooks share this information, it is more likely that QuickBooks will match an invoice to the wrong customer.

Additionally, Syncro and QuickBooks are very picky when searching for a customer on the Re-map page; the spelling, spacing, and capitalization all need to be exact to find the right match.

Failed Invoice Or Payment

If an invoice or payment fails, you'll see a red error appear on the Invoice or Payment page with a message. This will often describe the error and give you first steps on what to look for. We have a document for QuickBooks API Errors.

See also: QuickBooks API Errors.

Failed Sync

If a sync fails, navigate to the Invoice and select “Re-Sync to QuickBooks” from the Actions button menu. Wait a minute to see if the invoice/payment goes through.

Additionally, Syncro displays an error message on the page that comes directly from QuickBooks. You can then work to remediate the cause and try syncing again.

Wrong Person Displays on Invoice / Invoice Won't Sync

Note: In some cases you may also receive an “Incorrect or Missing QB ID Error.” 

These circumstances indicate that the Syncro Organization is not mapped to the corresponding customer inside QuickBooks and needs to be remapped. To clear this error and remap the customer, follow these steps:

  1. Navigate to the Organization's Details Page.  
  2. In the upper right, click on the book icon and select “View QB:”

    A page displays information for the Syncro customer Organization and its QuickBooks counterpart. If there is no QuickBooks ID for the customer, it will show as NOT FOUND:
  3. In the upper right, click Re-Map. This brings you to the Manually Map QuickBooks Customer page. 
  4. If needed, on the right, search for the correct customer. This is a search of QuickBooks Online that we present in Syncro. The names MUST be an exact match for their system to locate the customer. (Every space, punctuation, and upper/lower case matters!)
  5. In the search results that appear at the bottom, click the “Map to This” link.
    IMPORTANT: Seriously use CAUTION here. If you aren't careful you can link customers to the wrong person, so if you are uncertain, contact Support. 
  6. Navigate back to the invoice that won't sync. 
  7. In the upper right, click Actions > Re-Sync to QuickBooks and you should be good to go! 
    Note: This will remap the customer, but remapping the customer does not auto-assign an invoice to them. If an invoice had been synced to the incorrect customer, will have to resync it as described in Failed Sync.

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