Can I collect the remaining Shopify deposit balance using my own in-store payment processor?

If you're using Early Bird to take deposits online and you'd prefer to collect the remaining balance through your own in-store payment processor (e.g. a third-party terminal with a better rate), there is a workaround, but it involves a manual step and a workflow that Shopify hasn't explicitly documented end-to-end.

Here's what you need to know before setting this up.

Shopify's online deposits are limited to Shopify Payments and PayPal Express

Early Bird uses Shopify's Purchase Options (Selling Plans) API to enable deposits and deferred payments at checkout. This API only works with Shopify Payments and PayPal Express, so third-party payment gateways are not supported by Shopify for this flow.

Please note this is a Shopify platform constraint, not an Early Bird one. It affects two things:

  • Taking the deposit at checkout: only works if your store is on Shopify Payments or PayPal Express.
  • Auto-charging the remaining balance later: automatic capturing the deferred payment also requires Shopify Payments. If you're on a third-party gateway, the remaining balance would need to be collected manually.

If your store uses a third-party gateway for online sales, Early Bird's automated deferred payment collection won't work out of the box.

Check out our help article here to learn more about how Early Bird handles deferred payments on Shopify.

Using your in-store processor to collect the remaining balance

If you use Shopify POS and have a third-party terminal in-store, you can collect the remaining balance manually through POS using a custom payment method. Here's how:

  1. Go to Settings > Point of Sale > Payments in your Shopify admin and add your third-party terminal as a custom payment method (this tells Shopify to record the payment without processing it through Shopify Payments).
  2. When a customer is ready to pay the remaining balance, open their partially paid order in Shopify POS.
  3. Tap Collect payment and enter the remaining balance amount.
  4. Select your custom payment method (your third-party terminal name).
  5. Process the card on your external terminal as normal.
  6. Confirm and mark the payment as complete in Shopify POS.

Shopify will record the payment against the order, including the amount, payment type, and timestamp. But the funds are processed entirely by your external terminal. There are no additional Shopify fees for using a custom payment method.

Important note: This workflow (taking a deposit online via Early Bird and then collecting the remaining balance in Shopify POS) hasn't been explicitly confirmed by Shopify as a supported cross-channel flow. It's a reasonable workaround based on how both systems work individually, but we'd recommend testing it end-to-end before relying on it operationally. If you run into issues with POS not pulling through the correct remaining balance from an online deposit order, reach out to us and we can help troubleshoot.

Important note: Shopify POS won't automatically detect that your external terminal processed the payment. You'll need to manually confirm this in POS before the order is marked as paid.

If you don't use Shopify POS

If your in-store system is a separate ERP or POS that isn't connected to Shopify, the simplest path is:

  1. The customer pays the deposit online via Shopify as normal.
  2. When the customer pays the remaining balance in-store, or when you're ready to capture it for them, open their order in your Shopify admin.
  3. On the order page, click Collect payment and select a manual payment method (e.g. "Paid in store") to record the remaining amount as collected.
  4. This marks the Shopify order as fully paid without processing any funds through Shopify Payments.
  5. Continue your normal entry into your ERP or in-store system as you would today.

This keeps your Shopify orders complete and accurate, while your external system remains your source of truth for in-store transactions.

Important note: You will need a manual payment method set up in Shopify first. Go to Settings > Payments > Manual payment methods in your Shopify admin and create a custom one (e.g. "Paid in store" or "In-store terminal"). There are no additional Shopify processing fees for manual payment methods.

What your customers will experience

A few things to be aware of about your CX (customer experience) when using deferred payments:

  • Payment due date at checkout: Shopify always displays a payment due date to customers at checkout. This is enforced by Shopify and can't be removed.
  • Purchase option agreement label: Shopify also enforces displaying this, but you can customise the text in this label.
  • No deferred payment reminder email by default: Shopify doesn't have a reminder email template for deferred payments, customers won't automatically be reminded that a payment is coming.
  • Workaround for reminders: You can use Early Bird's pre-order shipping update email as a manual reminder to customers ahead of their payment due date.
  • Payment receipt after capture: Once the remaining balance is marked as paid, Shopify will send customers an email receipt confirming the payment.

Need help?

If you have further questions about collecting deposit balances through a third-party processor, email us at support@shopside.com.au and we'd be happy to walk through your specific workflow.

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