Connecting your QuickBooks account to Atoa is a great way to simplify how you send invoices and keep track of payments. Here’s how to get started, step by step.
Step 1: Access integrations in Atoa
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Log in to your Atoa dashboard.
If you’re new to Atoa, you can sign up in just a few minutes. -
From the left-hand menu, click on Settings.
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Select Integrations from the submenu.
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Find QuickBooks and click Set up now.
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Click the green Connect to QuickBooks button in the top-right corner.
Note: If you're already logged into QuickBooks, the connection will start right away. If not, you’ll be asked to log in and verify your account using an OTP for security.
Step 2: Authorise and configure QuickBooks
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QuickBooks will ask you to authorise Atoa’s access — click Connect.
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Choose the business you want to link to QuickBooks.
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If you only have one business, this step will be skipped.
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If you manage multiple businesses or locations, you’ll be asked to confirm which store you want to connect.
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Atoa will display your linked bank accounts. In QuickBooks, choose how to treat your payments:
Option 1: Treat as deposits
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Creates a dedicated account in QuickBooks to log all Atoa transactions.
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Your accountant can reconcile later using the bank feed.
Option 2: Treat as undeposited funds
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Stores transactions as undeposited funds.
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Ideal if you prefer to reconcile payments later.
Choose the option that best suits your accounting workflow.
Step 3: Create and send invoices in QuickBooks
Once your integration is active, here’s how to create an invoice with Atoa embedded:
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In QuickBooks, click Create Invoice.
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Select the customer you want to invoice.
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Fill in the details — due date, product/service, description, and amount.
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Click Save and send to preview the email.
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When ready, click Send and close.
Your customer will receive:
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An invoice email with an Atoa payment link
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A PDF version of the invoice (also with the payment link)
Step 4: Customer payment flow
When your customer clicks the Atoa payment link:
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They’ll be redirected to their mobile banking app to complete the payment securely.
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If they’re using a desktop, they can either:
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Continue on their phone, or
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Scan a QR code to pay from their mobile device.
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Once the payment is successful:
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In Atoa, you’ll see the payment details with the source marked as QuickBooks.
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In QuickBooks, the invoice status will automatically update to Paid, and the transaction will be marked as deposited.
And there you have it. Your QuickBooks and Atoa accounts are now connected and ready to help you simplify your invoicing and payments.
FAQs
Do I need a specific QuickBooks plan to use this integration?
You’ll need an active QuickBooks Online account. QuickBooks Desktop is not currently supported.
What happens if I disconnect QuickBooks from Atoa?
You’ll stop seeing Atoa payment links on your QuickBooks invoices, and payment updates will no longer sync between the two platforms. Past payment data will remain intact.
Can I still accept payments if QuickBooks is disconnected?
Yes, you can still accept payments through Atoa directly, but invoices created in QuickBooks won’t automatically include Atoa payment links or sync payment status.
Where can I see the source of a payment in Atoa?
Go to the Payments section of your Atoa dashboard. Payments that came through a QuickBooks invoice will be labelled with “QuickBooks” as the source.
Got a question?
Our UK-based Care Team is always here to help. You can reach us on our website Live Chat or by email at hello@paywithatoa.co.uk.