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QuickBooks Online: Setting up Your QuickBooks Online Integration


Download the Setup Guide HERE


In order to sync Clio with QuickBooks Online, you must first have a QuickBooks Online account. For more information about QuickBooks Online, and to get 30% off of your first 12 months, 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 (Unpaid) 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).
  • US Customers: We DO NOT sync Tax to the Sales Tax Center. It comes over as an individual line item that needs to be mapped to an appropriate Product or Service.
  • Canada & EMEA Customers: Clio Manage can import sales tax rate(s) from non-US versions of QuickBooks Online to perform sales tax calculations. Please see the Mapping Tax Rates (Non-US) section. 

The Integration at a Glance
Below is a high-level diagram showing you the key data flows between Clio Manage & QuickBooks Online. Please click on the image to expand it to full screen.


QuickBooks Online Suggested Settings
Linking Clio to QuickBooks Online
Setting up the Revenue Sync
Setting up the Trust Sync
Trust Check Printing
Mapping Tax Rates (Non-US)
Setting up Hard Costs Imports
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. Click the gear icon to open your Settings Menu, and select "Account and 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 me when I enter a bill number that’s already been used for that supplier", 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. 

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 "Connect" to the right of the QuickBooks Online Integration (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" button.


Once you have connected your accounts, you'll be able to configure the QuickBooks Online sync.


Setting Up the Revenue Sync

The first step in configuring your QuickBooks Online sync is to match each item in Clio to a "Product" or a "Service" that you create in your QuickBooks Online account. These can be created from the Products and Services section of QuickBooks Online, which you can access from the Settings menu in QuickBooks Online:


Please ensure that your QuickBooks Online "Products and Services" are connected to the appropriate Chart of Accounts before matching to items in Clio.

(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 Online.)

Note: To ensure the bank accounts are made available for mapping in Clio please refer HERE

Products and Services created in QuickBooks Online like you see here in QuickBooks Online...


...Can be matched to items in Clio using the dropdown menus in the "Map Clio data to QuickBooks Online products and services" section, as displayed below:


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 Online invoice.

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

You will now start to see your Clio Contacts and Bills synced to QuickBooks Online about every 30 - 60 minutes.


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. Beside the QuickBooks Online integration, Click "Configure Settings"
  4. Scroll down and check the "Export trust transactions" box
  5. Select the date that you would like to start syncing your trust from (defaults to the current date)
  6. Select the Clio trust account you want to sync with QuickBooks Online 
  7. Select the QuickBooks Online trust bank account you want to sync with Clio (as pictured below)
  8. Select the QuickBooks Online trust liability account you want to sync with Clio (as pictured below)
  9. Optionally, toggle Trust Disbursement or Trust Payment checkboxes, if needed
  10. Click "Save Sync Settings"

You can sync up to 15 (inclusive) trust accounts from Clio with QuickBooks Online. To learn more - visit the Multi-Trust Sync - QuickBooks Online Enhancement article. 


*Please note: By enabling the option"Payments made to Trust Requests and to Bills from a client account", will cause each transaction record from Clio to be synced into QuickBooks Online and will go as far back depending on the date entered below in the Export settings section "Trust Transactions dated on or after".

If you don't see a QuickBooks Online 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.

Check Printing

We know your firm may rely heavily on checks as the primary method to transfer funds out of trust accounts. This is why we’ve made it easy for you to enter trust records once in Clio Manage and automatically sync these over to QuickBooks Online and now print trust check disbursements quickly.

For a more in-depth look at Trust Check Printing, see here.

I’ve enabled ‘Trust Sync’ how do I start printing checks via Quickbooks Online?

  1. When you are ready to disburse funds from either the ‘account’ page or ‘transactions’ tab of the matters dashboard, you can disburse fund to a check, by selecting ‘Print Check via QuickBooks Online’
  2. Once the Print check via QuickBooks Online option is selected, you can then choose the recipient of the check. The recipient will appear as the payee on the check. The list of recipients contains contacts from the customer’s Clio account (e.g. returning the settlement fund to the client), as well as vendors from your Quickbooks Online account (e.g. writing a check to pay the court for the filing fee).
  3. After saving the transaction, Clio Manage will sync this disbursement over as a check in QuickBooks Online. You can find you check by logging into your QuickBooks Online account, then click on ‘+ New’ option from the top left corner, and then select ‘Print Checks’.
  4. You can then click ‘Preview and print’ to review the information before printing your check on pre-printed check paper. You can purchase these from QuickBooks Online here.

Mapping Tax Rates (Non-US)

Customers in Canada and EMEA (with non-US versions of QuickBooks Online) can select the ‘Include tax value with the corresponding line item’ option which allows Clio Manage to import sales tax rate from QuickBooks Online to perform sales tax calculations.

When Clio syncs a bill to QuickBooks Online, Clio will also update the sales tax amount in QuickBooks Online’s tax center and the default sales tax ledgers.


Here’s how this works:

  1. As the administrator of your firm, enable the ‘Export approved bills and recorded payments’ option of the QuickBooks Online Sync within Clio, and then select ‘Include tax value with corresponding line item’ under the Line item tax options.
  2. You can then map the sales tax rate(s) imported from the Sales Tax Centre in QuickBooks Online to primary, secondary, and tax-exempt dropdowns within Clio. This will allow Clio to perform sales tax calculations using the tax rate from QuickBooks Online when a bill is generated. Click on the ‘Save Sync Settings’ button after completing all the required fields. Mapping_Clio_Tax_rates_to_Quickbooks-2.png
  3. Once the Include tax value with the corresponding line item is selected, Clio will check the latest tax rate from QuickBooks Online every time a sync is performed (i.e. every few minutes). To ensure the rate is the same in both systems, Clio will override the primary and secondary tax values in Bill Settings with the values specified in QuickBooks Online and prevent them from being changed.
  4. After an invoice with sales tax is approved, Clio will sync the invoice to QuickBooks Online and update the corresponding tax amounts in the QuickBooks Online tax center. 

Setting up Hard Cost Imports

Expenses created in QuickBooks Online can be automatically imported into Clio for billing using the QuickBooks Online integrations "Import hard costs" feature: 


To set up the "Import hard costs" feature:

  1. Go to the Settings menu in Clio
  2. Click "Bill Syncing"
  3. Beside the QuickBooks Online integration, Click "Configure Settings"
  4. Scroll down and check the "Import hard costs" box
  5. Select the date that you would like to Import on or after
  6. Select the Account in QuickBooks Online that you'd like to import expenses from into Clio
  7. Click "Save sync settings"


Note: In order to use the Hard Cost Importer, you will need to have QuickBooks Online Plus or Advanced Plans.

For more detailed information on setting up and using the Import Hard Costs feature, see How Do I Use the ‘Hard Cost Import’ Setting?

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 "Disconnect from QuickBooks Online" button at the bottom right corner of the page: 


When Disconnecting Clio's access to your QuickBooks Online account, the sync maintains a memory of links between your synced invoices, Contacts, and payments will remain in case you want to reauthorize access at a later time.

After Disconnecting from a QuickBooks Online account, connecting to a different QuickBooks Online account will erase any memory of links with the previous QuickBooks Online account.

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