QuickBooks Online isn't designed to work with multiple Accounts Receivable (AR) and Accounts Payable (AP) accounts. QuickBooks Online encourages their customers to merge their accounts payable and receivable accounts into one.
In QuickBooks Online, the default Accounts Payable (AP) and Accounts Receivable (AR) accounts are selected during the initial account setup. Those are the accounts Bill.com transactions will sync to where applicable.
- If there are multiple AP and/or AR accounts in QuickBooks Online and Bill.com, transactions will still always sync to those initially set default accounts, unless they are deleted or merged in QuickBooks Online.
- If the initially set default accounts are deleted in QuickBooks Online, Bill.com will sync to the remaining active oldest AP and/or AR accounts, as those become the new default accounts in QuickBooks Online.
- QuickBooks Online won't allow users to delete the default AP and/or AR accounts without a replacement account having been created first, as that new account will become the new default in QuickBooks Online.
- QuickBooks Online will also not allow users to delete the default AP and/or AR accounts in QuickBooks Online if there are any transactions in the register. If there are transactions associated with the default AP and/or AR accounts, the new default AP and/or AR account(s) must be created first, then merged with the original default AP and/or AR accounts. The resulting accounts become the new default AP and/or AR accounts, to which Bill.com will sync transactions.
- If the old inactive default AP and/or AR accounts are reactivated in QuickBooks Online, they aren't restored as the defaults; whichever accounts were set as the new defaults as per the processes above will stay in place as the defaults unless those specific accounts are deleted or merged.
Please see the QuickBooks Online article Can I change the default A/R or A/P account in QuickBooks Online? for more information.