QuickBooks Online sync setup guide

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

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Sync overview

The following image shows what objects sync and in which direction.

Accounts under accountant consoles or signed up before 9/15/17

QBO sync image: payments 1 way


Accounts signed up after 9/15/17 not created under an accountant console

QBO sync image: payments 2 way


Pre-setup requirements

In order to complete the Sync Setup steps listed below, please note the following requirements:

  • QuickBooks Online: To connect the sync, a Primary Administrator or Company Administrator is required
  • Bill.com: A user with the Administrator or Accountant role is required (or custom role with manage company and sync permissions)

Connect the sync

  1. Select Set Up Sync on the Sync accounting software step of the Get Started page
  2. Select Connect to QuickBooks
    connect to QBO
  3. Enter your QuickBooks Online Primary Admin user ID and password, and Select Sign in
    QBO login creds
  4. Select the company in QuickBooks Online you want to sync to your Bill.com account and select Connect
  5. Select Set Up after the first import of chart of accounts completes
  6. Select the GL account from your chart of accounts that matches any bank accounts you added and select Next
  7. Select the GL account from your chart of accounts for uncategorized expenses and select Next
  8. Select Sync now to start the first full sync

The Sync is now connected.

Sync preferences

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

  1. Select Settings

  2. Under Sync, select Preferences

  3. Select Edit

  4. Select the QuickBooks Online accounts to use (we filled the list with your QuickBooks Online Chart of Accounts during the first sync) for the following settings (if applicable):
    Sync preferences

    • Sync Automatically
      • This ensures the sync is run at least once daily. The sync will run approximately 24 hours from the last sync time. However, the sync can always be run manually via the Sync Now button at any time.
    • Sync Only Approved Bills and Vendor Credits
      • Note: This setting is not reversible. Once turned on it can not be turned off.
      • This allows only those bills that have been fully Approved in Bill.com to sync to the accounting software
    • Enable 2-Way AP Payment Sync
      • This allows AP payments in your accounting software to sync to Bill.com
    • Unallocated Expense Account
      • This is where bills with no GL accounts specified in Bill.com will post to during the sync
    • Default Bank Account in Accounting Software
      • This is the default bank account used to record any payments made outside of Bill.com
    • Deposit To Account
      • Ex: Undeposited Funds is frequently used to record check payments received, but not yet deposited
      • This is the default account to record payments received outside of Bill.com
    • GL Account For Bank Account XXXX
      • This is where funds transfers for payments made/received through the specified bank account will post
    • Master In Case of Conflict
      • If a record is updated with different values in Bill.com and the accounting software before the next sync, only the values for the record set as master will be kept.
  5. Select Save


Accounting preferences

The following settings will be set based on settings within QuickBooks Online:

  • Show Account Numbers
  • Use Locations
  • Use Classes
  • Use Customer/Jobs in Payables
  • Use Items in Payables

To set additional or update preferences:

  1. Select Settings
  2. Under Accounting, select Preferences
  3. Select Edit
  4. Turn on any other settings that will need to be available in Bill.com
  5. Select Save
  6. Select Sync and Sync Now to run another sync

QuickBooks Online - Sync Setup - QuickBooks Online Sync Setup Guide - Sync now

The sync setup with QuickBooks Online is now complete.


Things to know

  • The sync will only pull in invoices created or updated within the last 90 days from the date the sync is first set up
    • If an invoice older than 90 days need to be synced over to Bill.com, select Edit and then Save on the invoice - this will trigger an update. Since the sync queries for recent updates, the next sync will now pull in that invoice due to the update.
  • The initial sync will bring in both active and inactive objects (chart of accounts, vendors, customers, etc.). This allows future updates to those objects to sync.

If you don't see the described feature available in Bill.com, you may not have access to the feature based on permissions for your role and/or your plan doesn't have this feature. If you wish to get access to the feature, please review the available plans for Bill.com and upgrade accordingly or contact the Administrator of your Bill.com account. Changes in monthly user fees may apply.