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Update QuickBooks Settings

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Updated at Aug 08, 2025
By Kali Patrick

Table of Contents

To Change Sync Settings for Invoices, Payments & Accounts To Update Tax Rates To Re-Map Payment Methods To Make Changes to Products To Re-Import Or Re-Send Data

Related Docs

  • Integrating QuickBooks
  • Set Up QuickBooks Online (QBO)
  • Troubleshooting Your QuickBooks Integration

After your initial QuickBooks Online setup, you can always return to the QuickBooks Settings Page to make changes. To return there, you can either:

  • Navigate to Admin > Integrations - App Center. Then select the QuickBooks tile, or
  • Add /quickbooks/settings to your URL. (For example: https://yourdomain.syncromsp.com/quickbooks/settings.)

The remainder of this document describes each of the settings, and where possible, provides best practices for use.

IMPORTANT: If you're unsure about how to update your QuickBooks settings, please get in touch with your bookkeeper or accountant who can advise you. 

To Change Sync Settings for Invoices, Payments & Accounts

At the very top, you'll see a list of checkboxes. These specify how data will be synced between Syncro and QuickBooks from this point forward:

The first three boxes are particularly important.

To Automatically Sync Payments From To Check These Boxes Notes
Syncro QuickBooks Online

Sync Invoices TO QuickBooks
 

Sync Payments TO QuickBooks (requires Invoices)

IMPORTANT: If you check these two boxes, be certain the “Sync Payments FROM QuickBooks” box is NOT checked. Syncing both ways will duplicate payment records, which will require manual correction. If you sync using the following row, then the "Sync Invoices TO QuickBooks" box must NOT be checked for the same reason.
QuickBooks Online Syncro Sync Payments FROM QuickBooks

 After you change this setting:

  • You must create the invoice in Syncro and have it sync to QuickBooks Online successfully.
  • You can then capture a payment on the QuickBooks Online side for that invoice and it will sync the next time the QuickBooks Online sync job runs. This job only runs once a day in the early evening Pacific Time. It will sync payments created up to 24 hours ago.

IMPORTANT: While you can apply multiple payments to single invoice, you can't apply one large payment to multiple invoices (i.e., split payments) to an invoice when syncing payments from QuickBooks Online to Syncro.

If you want to automatically convert payments created in QuickBooks Online to Syncro, then check the “Convert finished POs to Bills in QuickBooks” box. This means that whenever you set a PO to "Finished" Status, a Bill is automatically created in QuickBooks so you can pay your vendors.

When you check the "Sync all Syncro Products to QuickBooks" box, the product will sync to QuickBooks Online when it is created in the Products module in Syncro. Then it will show up properly on an invoice on the QuickBooks Online side. Note: The sync may take a few minutes so please be patient.

Next you'll find a list of dropdown menus that you can choose from so Syncro attaches income, expenses, and inventory to the correct accounts, and uses appropriate defaults:

Tip: Our recommendations are listed in each field's label, but if you're unsure, you should reach out to your bookkeeper or accountant for help.

When you check the “Sync Store Credit to QuickBooks” box, this will sync Syncro's store credit to QuickBooks Online. 

When you're finished, click Save QuickBooks Settings to save your changes.

To Update Tax Rates

Tax rates are created both in Syncro and in QuickBooks Online, then mapped to one another. All of the Syncro and QuickBooks tax rates, as they are currently mapped, show up here: 

To make changes, use the dropdown menus in the QB Online Association column. You may also need to configure Syncro's tax rates to adjust the mapping:

To Re-Map Payment Methods

Like tax rates, payment methods are created both in Syncro and in QuickBooks Online, then mapped to one another. All of the Syncro and QuickBooks payment methods, as they are currently mapped, show up here: 

You might need to re-map payment methods if you created a new QuickBooks Online payment method and want to use it in Syncro (or vice versa).

To make changes, use the dropdown menus in the QuickBooks Payment Method column. If you don't see the values you're expecting, click Import QuickBooks Payment Methods.

To Make Changes to Products

Like tax rates and payment methods, Products are created in both Syncro and in QuickBooks Online, then mapped to one another during your initial set up. 

Some reasons why you might need to re-map products include:

  • You created a new QuickBooks Online item and want to use it in Syncro,
  • You accidentally mapped to the wrong Product, 
  • A Product synced as “Miscellaneous” (or your default Product) and you want to map it to a more specific one.

To do this, click Check for Item Changes:

This prompts Syncro to register all your QuickBooks Online items, including products.

To Re-Import Or Re-Send Data

At the bottom of the QuickBooks Settings page you'll see two columns of buttons:

  • Import buttons: used to import data FROM QuickBooks INTO Syncro. This includes Customers, Products, Chart of Accounts, and Vendors.
  • Send All buttons: used to send Syncro data INTO QuickBooks. This includes Customers, Invoices, Payments, and Products.

      

During your initial set up, you may have been instructed to import your data using the QuickBooks Settings Wizard, or bypassed that and used the Send All buttons instead.

IMPORTANT: Unless someone in Syncro Support advises you to, avoid clicking these buttons after your initial set up. Ignoring this advice will generally lead to duplication and manual clean up. Furthermore, there's a limit on how frequently you can use these buttons because they query the entire data set each time. If these buttons are grayed out, it's because they've been clicked within the last 7 days. 

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