How to Connect QuickBooks Online

Written by Thomas Aronica (Super Administrator)

Updated May 21st, 2026

Connecting Biller Genie to QuickBooks Online links the two systems through Intuit's secure OAuth authorization flow. Once connected, your customers, items, accounts, invoices, sales receipts, and refunds stay in sync between the two systems with no manual reconciliation.

Before you start

Sign in to your Biller Genie merchant portal as an admin user.
Have access to your QuickBooks Online Master Admin credentials. The user authorizing the connection must be an admin on the QuickBooks Online company you want to sync.
Know which QuickBooks Online company file you want to connect — if you manage multiple companies through one Intuit login, you'll choose the company during authorization.

Multiple QuickBooks Online companies

If you manage more than one QuickBooks Online company under your Intuit login, the company you select during authorization is the one Biller Genie will sync with. Selecting the wrong company will pull unintended customers, items, and invoices into your Biller Genie account. Double-check the company name before clicking Connect.

Connect Biller Genie to QuickBooks Online

In the Biller Genie merchant portal, click Add-ons Marketplace.
Select the Accounting Software category and click the QuickBooks Online tile (or use the search field to find it).
Click Install.
Click Connect to QuickBooks. Biller Genie redirects you to Intuit's authorization page.
Sign in to Intuit as the admin user for the QuickBooks Online company you want to connect.
Review the access Biller Genie is requesting (full read and write access to your QuickBooks Online accounting data) and click Connect to authorize.
Intuit returns you to Biller Genie and the first sync begins automatically.

When the first sync finishes, you'll see a confirmation in the QuickBooks Online add-on page and your QuickBooks Online data will be available throughout the Biller Genie portal.

What happens during the first sync

After you authorize the connection, Biller Genie pulls your QuickBooks Online data into your Biller Genie account in the following order:

Chart of Accounts — income, expense, bank, and receivable accounts, plus their account types and subtypes.
Line items — your Products & Services (used on invoices and sales receipts), including the system items Biller Genie seeds for late fees, technology fees, surcharges, refunds, and third-party transactions.
Tax preferences and tax rates — your QuickBooks Online tax settings so taxable invoices route correctly.
Customers — your full customer roster, including email, billing address, and balance.
Invoices — recent open and recently paid invoices so you can start collecting on them in Biller Genie.
Sales receipts and refund receipts — recent payment activity for context and reconciliation.

After the first sync, Biller Genie keeps both systems in sync continuously through QuickBooks Online webhooks and a scheduled background job, so new invoices, payments, voids, and refunds flow back and forth without manual action.

Sync settings after connecting

Open the QuickBooks Online add-on page anytime to manage how Biller Genie interacts with your QuickBooks Online account:

Auto-sync — turn the ongoing background sync on or off. Off pauses automatic updates between the two systems.
Sync CC emails to QuickBooks Online — push the CC email addresses you've set on customers in Biller Genie up to the corresponding customer in QuickBooks Online.
Display line-item groups — control whether grouped line items show on the invoices Biller Genie creates in QuickBooks Online.
Commodity code — set a default UNSPSC commodity code for items synced from Biller Genie to QuickBooks Online.
Full resync — trigger a fresh pull of your QuickBooks Online data when something looks out of date. The resync runs in the background and is audit-logged for your records.

Chart of Accounts mapping is now separate

The Chart of Accounts mapping tool lives in the accounting-software section of the merchant portal. Use it to control which QuickBooks Online accounts Biller Genie writes to for sales, refunds, sweep deposits, and Undeposited Funds. Read the Chart of Accounts article.

Managing the connection inside QuickBooks Online

QuickBooks Online also lets you view and manage every connected third-party app from within your QuickBooks Online company. From the QuickBooks Online navigation, open Apps (or the gear icon's Manage Apps option, depending on your view) to see Biller Genie alongside any other connected apps. From there you can review what access has been granted, see when each app last connected, and disconnect any app directly from QuickBooks Online.

For the canonical, up-to-date instructions on managing connected apps inside QuickBooks Online, see Intuit's help article: Manage your apps in QuickBooks Online (Intuit Help).

Disconnecting QuickBooks Online from Biller Genie

In Biller Genie, go to Add-ons and select QuickBooks Online.
Click Disconnect from QuickBooks.
Biller Genie revokes the Intuit authorization token, stops the background sync, and the QuickBooks Online tile returns to its install state in the Add-ons Marketplace.

Disconnecting from inside Biller Genie also clears the authorization on Intuit's side. If you disconnect from inside QuickBooks Online instead (under Apps), Biller Genie detects the revocation on the next sync attempt and treats the connection as disconnected.

Reconnecting after a credentials change

If your Intuit or QuickBooks Online login credentials change, the authorization between Biller Genie and your QuickBooks Online company may need to be re-established. If your sync stops working after a credentials change:

In Biller Genie, go to Add-ons and select QuickBooks Online.
Click Disconnect from QuickBooks (if the connection is still listed).
Click Connect to QuickBooks and follow the connect steps again from step 3 of the Connect Biller Genie to QuickBooks Online section above.

FAQs

Does connecting Biller Genie change anything in my QuickBooks Online?

Connecting itself doesn't change your QuickBooks Online data — it only authorizes Biller Genie to read and write on your behalf. The first sync pulls your existing customers, items, accounts, and recent invoices into Biller Genie. Going forward, Biller Genie writes payments, refunds, and updates back to QuickBooks Online as you process them, the same way you'd write them manually.

I selected the wrong QuickBooks Online company. How do I switch?

Disconnect using the steps above, then click Connect to QuickBooks again. During authorization, Intuit will let you pick a different QuickBooks Online company from your Intuit login. Make sure you're selecting the correct company before clicking Connect.

My sync stopped working — what should I check first?

Three quick checks: (1) is the QuickBooks Online add-on still showing as connected in Biller Genie? (2) Is the Auto-sync setting turned on? (3) Did any Intuit or QuickBooks Online credentials change recently? If you changed credentials, reconnect using the steps in the previous section.

How do refunds and voids flow back to QuickBooks Online?

When you void or refund a transaction in Biller Genie, the corresponding record is written back to QuickBooks Online automatically: a Refund Receipt applied to the customer for a refund, or a voided sales receipt for a void. See How to Refund a Payment and How to Void a Payment.