QuickBooks Online Sync: FAQ

What Syncs?

Accounts under accountant consoles or signed up before 9/15/17
QuickBooks Online sync flow 1 way payments

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

QuickBooks Online sync flow 2 way payments


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.

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. Click Sync Now


  • Option two
    1. Click the sync icon
    2. Click 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. Click the gear icon
    2. Under Sync, click Preferences
    3. Click the edit icon
    4. Select Sync Automatically
    5. Click Save

Do credit memos sync?

  • Unapplied Credit Memos
    • Do not sync for accounts signed up for before 1/15/19
    • 2 way for accounts signed up for after 1/15/19
  • Partially or Fully applied Credit Memos
    • Do not sync for accounts signed up for before 1/15/19
    • 1-way from Bill.com to QuickBooks Online for accounts signed up for after 1/15/19

Note: Credit memo application, that partially pays an invoice, will not sync until the invoice is paid in full

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

Only accounts signed up after 9/15/17 have 2-way payment sync.