QuickBooks Online sync: Frequently asked questions (FAQ)

What Syncs?

QuickBooks Online 1 way payments sync flow


Why are some of my bills/invoices not showing up in Bill.com from QuickBooks Online?

  • Make sure you have set your sync preferences (Unallocated Expense, Unallocated Income, Bank account GL…)
  • Only unpaid Bills and invoices will sync from QuickBooks Online to Bill.com. We do not sync historical Paid or Partially Paid bills or invoices.
  • Only USD Currency is supported by Bill.com, hence Bills and Invoices must be in this format in order to sync over.
  • Bill and Invoice Numbers are required in order for these to sync from QuickBooks Online into Bill.com.
  • Items and transactions from QuickBooks Commerce do not sync.

How do I reconcile my Bill.com payments?

Using the Bill.com clearing accounts and/or Funds Transfer detail report.

How do I track the application of vendor credits?

When applying a vendor credit in Bill.com, the application will sync back to QuickBooks Online based on payment status of the bill.

How do I stop bills/invoices syncing from QuickBooks Online?

By default, transactions have a 2-way sync. If you want them to sync only from Bill.com to QuickBooks Online, please contact Customer Support.

How can I view my bill documents from QuickBooks Online?

Documents do not sync between Bill.com and QuickBooks Online.

How and where do I sync?

Syncing can be performed from within Bill.com in two different ways.

  • Option one
    1. Hover over the sync icon at the top of any Bill.com page
    2. Select Sync Now


  • Option two
    1. Select the sync icon
    2. Select Sync Now

When syncing, do I have to sit and watch?

You can leave the sync screen at any time and continue to work in Bill.com. The sync icon at the top of the page in Bill.com will show your sync progress.

Do I need to sync manually every time?

While you can sync manually at any time, the sync will automatically run approximately 24 hours after your most recent sync. We suggest syncing daily to ensure QuickBooks Online and Bill.com are up-to-date, and financial reports are accurate.

To turn on Auto Sync:

  1. Select Settings
  2. Under Sync, select Preferences
  3. Select the edit icon
  4. Select Sync Automatically
  5. Select Save

Why aren't the payments I record in QuickBooks Online syncing to Bill.com?

Payments only sync in one direction, from Bill.com to QuickBooks Online by default. Payments recorded in QuickBooks Online won't sync over to Bill.com, unless you enable the option to sync 2-ways in sync preferences.

  1. Select Settings
  2. Select Preferences under Sync
  3. Select the edit icon
  4. Select Enable 2-Way Payment Sync
  5. Select Save