Learn from the best and brightest in legal, technology, and beyond! Join us at the 2019 Clio Cloud Conference — San Diego | October 21-22, 2019.

QuickBooks Online: Setting up Your QuickBooks Online Integration

The Quickbooks Online integration is available to subscribers of our Legacy, Loyalty, Boutique, and Elite plans.

You can upgrade to the Boutique or Elite plan in the app, or if you’re interested in seeing how this feature can work for your law firm feel free to contact us by email or give us a call at 1-888-858-2546 (choose option #1).

In order to sync Clio with QuickBooks Online, you must first have a QuickBooks Online account. For more information about QuickBooks Online subscription levels, or to try it for free, click here. It can take up to 24 hours for the initial sync to complete, but the sync will occur periodically every five minutes.

The current integration allows users to:

  • Sync Contacts between Clio and QuickBooks Online
    • Contacts/Customers originating from QuickBooks Online will not be synced over to Clio and must be manually entered into Clio.
    • Only Contacts with Approved invoices (Awaiting Payment) will sync from Clio to QuickBooks Online.
    • Once synced, if you update a Clio Contact in either application it will be updated in the other.
  • Sync invoices from Clio to QuickBooks Online (one-way from Clio to QuickBooks Online). Payments and credit notes applied to Bills in Clio will also be synced to QuickBooks Online.
  • Sync trust transactions from Clio to QuickBooks Online (one-way from Clio to QuickBooks Online).
  • We DO NOT sync Tax to the Sales Tax Center. It comes over as an individual line item that needs to be mapped to the appropriate Product or Service.


QuickBooks Online Suggested Settings
Linking Clio to QuickBooks Online
Setting up the Trust Sync
Revoking Access to QuickBooks Online

QuickBooks Online Suggested Settings

To ensure that invoices sync properly between your Clio and QuickBooks Online accounts and to prevent the duplication of invoice numbers, there are two settings that should be enabled in your QuickBooks Online account before linking to Clio.  

Please follow these steps to enable "Custom Transaction Numbers" in your QuickBooks Online account:

  1. Open your "Company Settings"
  2. Click on the "Sales" tab then click on the pencil icon to edit the "Sales Form Content" settings.
  3. Check the box beside "Custom Transaction numbers", then click on the "Save" button.
  4. Click on the "Advanced" tab then click on the pencil icon to edit the "Other preferences" settings.
  5. Check the box beside "Warn if duplicate bill number is used", then click the "Save" button.

If starting in QuickBooks Online before Clio, you should adjust your first invoice number in Clio to be higher than the last invoice in QuickBooks Online. This is because both systems will automatically number your first invoice as number 1, and to avoid duplication errors this should be adjusted. More on editing invoices can be seen here.

Note: It is recommended to make any payment edits or deletions in Clio as this will sync to Quickbooks Online. Any edits or deletions made in Quickbooks Online will not sync to Clio. More can be read here.

Note: If you have a bank feed set up in QuickBooks Online, you may want to exclude Disbursements and Bill payments from Trust when setting up your Trust Sync. Otherwise, you may end up duplicate transactions in QuickBooks Online.

Linking Clio to QuickBooks Online

To sync your Clio account to your QuickBooks Online account, go to "Settings" and click on "Bill Syncing", then click "QuickBooks Online" from the links across the top.

Note that only account administrators can access "Bill Syncing" in the Settings panel.

To grant Clio access to your QuickBooks Online account, click the "Connect to QuickBooks" button.

Once you have synced your accounts, "QuickBooks Online Sync Settings" will become available.


Match each item in Clio to a "Product" or a "Service" that you set up in your QuickBooks Online account. These are the accounts from your Chart of Accounts in QuickBooks Online and should be set up appropriately for your jurisdiction. The examples shown in this article may not apply to your practice. Clio recommends that you consult with an accountant when setting up your Products and Services in QuickBooks.

Please ensure that your QuickBooks Online "Products and Services" are connected to the appropriate Chart of Accounts before setting up these matches in Clio.


By default, QuickBooks Online will separate each tax charge on a bill as its own line item. Keep "Aggregate line item taxes on QuickBooks Online invoices" checked to have the sum of each line item tax combined on the QuickBooks invoice.

Once you have matched all item types, click "Update Sync Settings".

You will now start to see your Clio Contacts and Bills synced to QuickBooks Online about every 30 - 60 minutes. A summary of the Sync Status can be found on your Bill Syncing page.


For tips on using the QuickBooks Online integration, click here.

Setting up the Trust Sync

The Clio Trust sync is a one-way, automatic export of trust transactions from Clio to QuickBooks Online. This includes:

  • Manual additions or subtractions of trust funds
  • Matter to Matter transfers of trust funds
  • Payments made to Trust Requests
  • Payments on Revenue Bills from a trust account
  • Edits to any of these transactions

Prior to setting up the QuickBooks Online Trust sync in Clio, ensure that you have the correct trust accounts set up in QuickBooks Online. You need to have two accounts, specifically:

  • A bank account (category: "bank") with detail type: Trust Account
  • A liability account (category: "other current liabilities") with detail type: Trust Accounts - Liabilities

For more information on setting up accounts with different detail types in QuickBooks Online, click here.

To set up the QuickBooks Online Trust sync:

  1. Go to the Settings menu in Clio
  2. Click "Bill Syncing"
  3. Click "QuickBooks Online"
  4. Scroll down (past the settings for the QuickBooks Online Bills Sync)
  5. Select "Export Trust from Clio to QuickBooks Online"
  6. Select the Clio trust account you want to sync with QuickBooks Online
  7. Select the QuickBooks trust bank account you want to sync with Clio
  8. Select the QuickBooks trust liability account you want to sync with Clio
  9. Select the date that you would like to start syncing your trust from (defaults to the current date)
  10. Click "Update Sync Settings"


If you don't see a QuickBooks trust liability account in the dropdown, ensure that you have a trust liability account designated in QuickBooks Online. For information, see the "Account Detail Types" article on the QuickBooks Online support site.

For information on using the QuickBooks Online Trust Sync, see the "Using the QuickBooks Online Integration" article.

Revoking Access to QuickBooks Online

To remove the connection between your Clio and QuickBooks Online accounts, go to the QuickBooks Online sync settings in Clio and click the "Revoke Access" link. 

When revoking Clio's access to your QuickBooks Online account, you have the option to just revoke Clio's access or purge it completely. When you revoke access, the links between your synced invoices, Contacts, and payments will remain in case you want to reauthorize access at a later time. The "Revoke and Purge" option will delete all of the links between your Clio Contacts, invoices, and payments; and those in QuickBooks Online. This will allow you to reconnect your QuickBooks Online account to Clio with a clean start. Please note that you should only choose the "Revoke and Purge" option if you are also purging your QuickBooks Online account.

Was this article helpful?
This information is confusing or wrong
This isn't the information that I was looking for
I don't like this functionality