How to connect Atoa with your Shopify account

Integrating Atoa with your Shopify store lets your customers pay you directly through their bank app, quickly, and securely. Follow these steps to get set up.

Prerequisites

Before you begin, make sure:

You’ve signed up for Atoa and connected your business bank account.
Your business is verified in Atoa.
The Payouts feature is enabled on your account so Shopify payments can be settled at the end of the day, and so you can issue instant refunds.

Step 1: Install the Atoa Payments App to Shopify

Go to Settings from the left-hand menu on your Atoa dashboard.

Click on the Integrations tab.

Under the Shopify option, click Set up now.

Then click Go to Shopify. This will take you to the Shopify App Store.

Click Install to add the Atoa Payments app to your Shopify store.

If you’re not already logged into your Shopify account, you’ll be prompted to sign in first.

Note: If you don’t have the Payouts feature enabled yet, you’ll see a Contact us button instead of Go to Shopify. Our team will get in touch and enable end-of-day Payouts for your account. Once that’s done, we’ll share the Shopify installation link with you.

Step 2: Connect the Atoa store with Shopify

Once installed, you’ll be taken to your Shopify dashboard. The app will now appear under Apps and sales channels in your Shopify dashboard.

On your Atoa dashboard, tick the consent box and click I understand to authorise the connection.

If you manage multiple Shopify stores, you’ll be asked to choose which one to connect. If you skip this step, payments will be reflected under your default store location.

Step 3: Activate Atoa Payments in Shopify

You’ll be redirected again to Shopify, specifically to the Atoa Payments section under Payments.

Before going live, enable Test Mode and simulate different payment scenarios (failed, pending, completed) to make sure everything works.

Atoa Payments will now appear under Supported Payment Methods in your Shopify Payments settings.

Go Live Checklist

Test failed, pending, and completed payment scenarios in Test Mode.
Confirm your bank account is connected and KYB verified in Atoa.
Ensure the Payout feature is enabled — Shopify payments will be settled by the end of the day.

That’s it! Your customers will now be able to pay using open banking through Atoa. At checkout, they’ll see a QR code which they can scan to complete the payment using their banking app.

FAQs

How to check if I’ve received a Shopify payment?

You can check payments in both your Shopify Admin Dashboard and your Atoa dashboard/merchant app at the connected store location.

In Atoa, click on the notifications bell icon on the top right of the dashboard, or

Go to Payments from the left-hand menu. Look for transactions labelled Shopify under the Source column.

Click on the transaction to view full payment details.

How do I issue a refund?

In your Atoa dashboard, go to Payments and click on the relevant transaction. Then click on either the Payment ID or the Refund button.

This will take you to your Shopify Orders page.

Select the order and click Refund at the top of the page. Choose the items to refund and click the final Refund button on the right to confirm.

The refund timeline will appear below, and the status will update in both Shopify and your Atoa dashboard.

Note: Refunds do not work in Test Mode. They are only available when Payouts are enabled.

How do I disconnect Atoa from Shopify?

In the Atoa dashboard, go to Settings > Integrations.

Under Shopify, click Manage, then click Disconnect.

Confirm the disconnection by clicking Disconnect again on the pop-up.

Alternatively, you can remove the Atoa Payments app directly from your Shopify Admin Dashboard.