QuickBooks Desktop sync setup guide

This guide will walk you through setting up the sync with QuickBooks Desktop.

Tip: Back up your QuickBooks company file before proceeding.

Table of Contents

Pre setup requirements

  • Make sure anyone with shared access to the QuickBooks file to be synced is logged out
  • QuickBooks needs to be in single-user mode
    • Select File, if Switch to Multi-user Mode is available, the file is already in single-user mode.
  • Exit QuickBooks
  • QuickBooks Admin login credentials - this is required to connect the sync
  • Cashflow360℠ user in Administrator, Accountant or custom role with Sync permission
  • Administrator rights to install programs to computer or server

Install sync dashboard

The sync dashboard needs to be downloaded and installed in the same location/drive as the QuickBooks program to sync between Cashflow360 and QuickBooks Desktop.

The QuickBooks company file doesn't need to be located in the same location to sync.


  • The sync dashboard requires Microsoft .NET framework 4.6 to be enabled to run properly. If on .NET framework 4.7 or later, 4.6 may still need to be manually enabled.
  • The sync dashboard has been verified to be compatible with QuickBooks Desktop 2014 and later, but may still work with older versions.

QuickBooks program installed on local computer

  1. Download the Quickbooks Desktop sync dashboard (~988 KB)
  2. Open the .exe file
  3. Select Next
  4. Select the drive that the QuickBooks program is installed on
  5. Select Install
  6. Select Next to confirm installation completion
    • A shortcut will be created on your desktop

QuickBooks program installed on Server or Hosted Server

Instructions on the installation of the sync dashboard will need to be provided to your I.T. administrator or hosting provider administrator so that the sync dashboard can be installed on your behalf.

Connect the Sync

  1. Open the Bill.com sync dashboard from the shortcut added to the desktop

  2. Open QuickBooks and log in to the company file as Admin and in single user mode

  3. In the profile editor box, select Next
    sync_dashboard_and_profile editor

  4. Sync dashboard will auto detect the file path of the QuickBooks company file that is open, select Next

  5. In QuickBooks, on the Application Certificate, select Yes, always; allow access even if QuickBooks isn't running

    • If there are multiple users on the company file, next to Login as: select Admin
  6. Select Continue

  7. Select Done to confirm access

  8. Enter Bill.com login credentials or sync token

    • If using a Bill.com powered solution through a bank/financial institution, the sync token will be required to connect the sync
      1. In Cashflow360, select settings
      2. Select Tokens under Sync
      3. Select New
        • Name will auto-populate (this is a one-time use object)
      4. Select Save
        • The token will be generated (also a one time use object)
      5. Write down or copy & paste the username and token, before navigating away from this page, as it is only shared one time
      6. On the Sync Dashboard:
        • Email = Token Name
        • Password = Token
  9. Select the Cashflow360 Organization name to sync to

  10. In the sync profiles box, select the profile to sync

  11. Select Sync

The sync is now connected.


The sync brings everything needed for payables and/or receivables from QuickBooks into Cashflow360: accounts, vendors, customers, items, departments (classes), jobs (customer: jobs), and your book balance.

The first sync might take a while, depending on the size of the QuickBooks company file. Future syncs will be much faster, and the QuickBooks company file won't need to be open.

Sync preferences

After the first sync completes, fill out sync preferences. Some fields will be pre-filled, review to make sure the correct accounts have been selected.

  1. In the One last thing box, select Ok or the X to close the box.


  1. Close the browser window that opens automatically.
  2. Select Settings
  3. Select Preferences under Sync
  4. On the Sync preferences page, select the checkbox to move transactions to QuickBooks Pro/Premier.
  5. Select the QuickBooks accounts to use (we filled the list with your QuickBooks Chart of Accounts during the first sync) for the following settings: *Accounts Payable *Unallocated Expenses *Default bank account in accounting software *GL accounts for any bank accounts already added to Cashflow360
  6. Select Save

The sync setup is now complete.

Enable 2-way bill sync

By default, our integration with QuickBooks Desktop only supports bill creation and edits in Cashflow360, which then syncs over to QuickBooks Desktop. If you would like bill creation and edits in QuickBooks Desktop to also sync to Cashflow360, you'll need to enable 2-way bill sync.

Note: This setting can't be disabled once enabled

To enable, users with the Sync with Accounting System permission will:

  1. Select Settings
  2. Select Preferences under Sync
  3. Select Edit
  4. Select the box next to Sync bills from QuickBooks desktop to BDC
  5. Select Yes to confirm
  6. Select Save

Accounting preferences

To set additional preferences for reporting and tracking:

  1. Select Settings
  2. Under Accounting, select Preferences
  3. Select Edit
  4. Set preferences
    • Classes in QuickBooks are called Departments in Cashflow360
    • Locations don't sync with QuickBooks Desktop
  5. Select Save