How to edit the remaining deferred payment for Shopify pre-orders?

After a customer places a pre-order with a deposit on Shopify, you might need to edit the remaining deferred payment (balance) they'll be charged later. This commonly happens when:

Tariff changes increase your landed costs
Variable shipping fees change based on destination
Supplier prices increase before fulfillment
Currency fluctuations affect your final costs

Unfortunately, Shopify doesn't allow you to directly edit it for pre-order products. In this help article, we'll walk through the why and how to use a workaround to edit the remaining balance instead.

Why you can't directly edit the remaining balance on Shopify

When a customer places a pre-order with partial payment (e.g., 50% deposit), Shopify creates a fixed payment schedule:

First payment: The deposit amount (captured immediately)
Second payment: The remaining balance (captured on your selected specified date)

Shopify's limitation: Once the pre-order is placed, you cannot change the remaining balance amount for the pre-order product itself. This is a Shopify platform restriction, not an Early Bird limitation.

Solution: Add the cost difference as a custom line item

Since Shopify won't let you edit the remaining balance directly, you can add the cost difference as a separate line item (like shipping adjustments or tariff fees). When the deferred payment date arrives, Shopify will automatically capture the original remaining balance PLUS any additional line items you've added.

Here's an example scenario from an actual support ticket we've helped:

The merchant had an original pre-order product price of $480
They collected a 50% deposit of $240 for the pre-order
This meant the original remaining balance was $240
However, they had a new product price $520 due to tariffs
Their desired new remaining balance: $280

The workaround:

The merchant added a $40 custom line item, so when Shopify captured the deferred payment, it charged the $240 (original balance) + $40 (custom line item) = $280 total.

Step-by-step to edit the remaining deferred payment on Shopify

Step 1: Edit the order in Shopify Admin

Go to Shopify Admin > Orders
Click on the specific order you want to adjust
Click Edit

Product page for CS3trom Astro Pro Electric Bike showing $3,000 AUD price with two purchase options: pay in full today with 20% discount, or pay 50% deposit to reserve with remaining balance charged on February 17, 2026 — For this help article example, let's place a 50% deposit on an electric bike as a pre-order.

Shopify order #1075 showing a pre-order for CS3trom Astro Pro Electric Bike with 50% deposit paid ($1,500) and remaining balance of $1,510 due February 17, 2026 — After the pre-order is placed, we can visit the specific order and can see the $1,500 deposit has been paid, with the $1,510 remaining balance scheduled for February 17, 2026.

Shopify edit order screen with buttons to add product or add custom item, showing the pre-order item and payment details with option to edit shipping fees — Click "Edit" on the order, and this is what you'll see.

Step 2: Add the cost difference

For a product price increase:

Click Add custom item
Name it clearly (e.g., "Tariff adjustment" or "Additional product cost")
Enter the cost difference amount (e.g., $40)
Optionally add an internal note explaining the reason with your team

Add custom item modal filled in with — Enter a clear name (e.g., "Tariff prices") and the cost difference amount ($50.00 in this example).

For a shipping cost adjustment:

Click Edit shipping fees
Add a shipping fee to reflect the actual cost
Shopify will calculate the total automatically

Edit shipping fees modal showing Standard shipping at $10.00 with option to add additional shipping fee — Alternatively, if adjusting shipping costs, click "Edit shipping fees" and "Add shipping fee".

Add shipping fee modal with — Enter a descriptive title (e.g., "Extra shipping costs") and the additional amount.

The custom line item and any new shipping costs will get added to the order total. When Shopify automatically captures the deferred payment on your specified date set in Early Bird, it will charge the original remaining balance + any additional line items as your customer's new remaining balance.

Step 3: Notify your customer

After making the edits, Shopify will prompt you to update the order and you can choose to send an invoice to the customer. The invoice will be sent to the customer's email they used during their initial checkout.

Edit order screen showing updated total of $3,075 with custom tariff prices line item ($50) and extra shipping costs ($15) added, plus — After adding the custom items, the order now shows the updated total. You can notify customers of the price change via the "Send invoice to customer" checkbox.

Important: Customers won't be automatically notified about price changes unless you send them an invoice. We recommend sending the invoice so they're aware of the new total before the deferred payment is captured.

Step 4: What the customer sees

When you send the invoice, your customer will receive:

An updated order summary showing the new line item(s)
The new total amount
The updated remaining balance to be charged

The customer can choose to Pay Now, or wait for the original due date, which will also be listed.

When the deferred payment date arrives, Early Bird will signal to Shopify to automatically capture the new total (original remaining balance + the custom line item amount) for you.

Shopify invoice showing payment of $1,575 due February 17, 2026, with order summary displaying CS3trom Astro Pro Electric Bike at $3,000, Tariff prices custom item at $50, shipping $25, for updated total of $3,075 with $1,500 already paid — If you send the invoice email, customers can see exactly what they're being charged before the automatic payment capture.

Need help?

If you have further questions about capturing deferred payments for your Shopify pre-orders, feel free to reach out to us at support@shopside.com.au!