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Integrating QuickBooks

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Updated at Jun 15, 2026
By Kali Patrick

Table of Contents

How the Integration Works Supported Features Payment Sync Direction Not Supported

Related Docs

  • Set Up QuickBooks Online (QBO)
  • QuickBooks Desktop Setup and Help
  • Converting from QuickBooks Desktop to QuickBooks Online

Integrating QuickBooks with Syncro streamlines your financial processes by automatically syncing invoices, expenses, and payments. This saves time, reduces errors, and provides real-time financial visibility. These in turn simplify bookkeeping, enhance financial reporting, and ease tax preparation.

Once your QuickBooks account is properly set up, you can choose to integrate either the QuickBooks Online (QBO) or the QuickBooks Desktop (QBD) version. 

How the Integration Works

The QuickBooks integration syncs data from Syncro to QuickBooks unless otherwise noted. It is not an ongoing two-way sync. 

There are two exceptions to this. First, at initial setup, customer data can be imported from QBO into Syncro. Second, payments can optionally be configured to sync from QuickBooks into Syncro (see Update QuickBooks Settings). For initial setup details, see Set Up QuickBooks Online. After setup, customer data only flows from Syncro to QuickBooks.

Supported Features

Feature QBO QBD
Live Updates √ 
(updates sent immediately)
√ 
(syncs when the QB Web Connector automatically runs or when you manually run it)
Tax Groups support for complex tax configurations √  
Imports/Exports
Export all Organizations to QB * *
Import Organizations from QB  * *
Export all Products to QB √  
Syncs/Updates
Sync Organization records when an Organization is updated ** **
Sync Sub-Customers
(These map as Organizations in Syncro.)
*** ***
Sync End Users  *** ***
Sync Invoices to QB when updated in Syncro √ √
Sync Organization records when an Invoice is updated √ √
Sync Invoices with $0 totals √  
Sync Purchase Orders (POs) and Bills √  
Sync Products (as items) when a Product is created and added to an Invoice √  
Sync Products (as items) when a Product is updated √  
Sync Customer Purchases √  
Update creation and payment dates when clicking "Force Update" button √  
Creations & Deletions
Create Purchase Order Bills when PO is marked finished in Syncro √  

For payment sync details, see Payment Sync Direction below.

Annotations:

  • * Customer import/export is a one-time manual operation performed during initial setup. After setup, customer data only flows from Syncro to QuickBooks. 
  • ** Any new customers or updates made to a customer will not sync until they receive an invoice to sync. If you want to update a customer without creating an invoice, you need to make changes in both Syncro and QuickBooks.
  • *** Syncro only supports parent customer/Organization syncing in the integration.

Payment Sync Direction

By default, payments sync from Syncro to QuickBooks. QBO also supports syncing payments from QuickBooks into Syncro, with some limitations:

Payment Type Syncro → QB QB → Syncro
Payments √ QBO, √ QBD √ QBO only
Overpayments (a Payment greater than the Invoice amount) √ QBO, √ QBD  
Partial Payments (multiple Payments to complete an Invoice) √ QBO, √ QBD  
Split Payments (one Payment applied to multiple Invoices) √ QBO, √ QBD  
Store Credit as Credit Memo √ QBO, √ QBD  

Note: You cannot enable both "Sync Payments TO QuickBooks" and "Sync Payments FROM QuickBooks" simultaneously, as doing so will create duplicate payment records. See Update QuickBooks Settings.

Not Supported

  • Sync Invoices to Syncro when updated in QuickBooks
  • Sync Refund Invoices (Invoices with refunds need to be adjusted manually in QuickBooks.)
  • Sync Split Payments from QuickBooks to Syncro (Not supported even when “Sync Payments FROM QuickBooks” is enabled)
  • After moving a Payment in QuickBooks from one Invoice to another, sync the change to Syncro
  • Sync Credit Memos in QuickBooks back to Syncro
  • Sync Purchase Order shipping, notes and tax
  • Sync inventory quantity on Stock Takes
  • Sync Categories

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