How to Issue a Shopify Partial Refund?

Returns and refunds have a bigger impact on Shopify revenue than many merchants realize. Shoppers are expected to return about $849.9 billion in goods in 2025, and around 93% review a store’s return policy before buying. This means the way you handle refunds can affect sales, not just customer support. A Shopify partial refund is one piece of that picture: you return part of an order’s value while the customer keeps the remaining items. It helps resolve the issue without giving up the entire sale. 

I am Charlie Ngo, an eCommerce expert at BOGOS, and I make these calls the way any store owner has to. In this blog post, I’ll explain what a partial refund is, when to use one, how to issue it in Shopify, and how to reduce avoidable refunds. 

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TL;DR

• A partial refund returns part of an order’s value while the customer keeps the rest.
• You can issue a Shopify partial refund with this flow: Go to Orders -> open the order, click Refund, then set item quantities or edit the Refund amount field for a custom sum. 
• Shopify caps a shipping refund at what was charged and recalculates tax automatically. 
• With Shopify Payments, card processing fees are not returned on any refund, so build the lost fee into the amount you give. 
• A customer can still charge back the full order value after a partial refund, so keep the refund record and Acquirer Reference Number as evidence.
• Cut avoidable refunds by fixing sizing, packaging, and delivery expectations, tracking refund reasons, and using gift or bundle offers to turn goodwill into repeat orders.

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1. What A Partial Refund Is

A partial refund returns part of an order’s value instead of the whole thing. The customer keeps what they want, you keep the rest of the sale, and the order status changes from “Paid” to “Partially refunded.”

Here is what a partial refund lets you do:

• Refund a single item, several items, or a custom dollar amount.
• Refund shipping on its own.
• Issue more partial refunds on the same order later, up to the original order total.

A full refund and a partial refund work differently. A full refund sends back the entire payment and closes the order, so you cannot refund it again. A partial refund sends back only the amount you choose and keeps the order open. The table below shows the difference at a glance: 

	Full refund	Partial refund
Amount returned	Entire order	A portion of the money
Use case	-Out-of-stock items-Full returns-Cancellations	-Minor damage-Delays-Price adjustments-Partial returns
Item status	Refunded	Partially refunded
Shipping & taxes	Full fees	Fees adjusted based on the refund amount
Transaction fees	-Shopify Payments: not returned-Third-party gateway: 100% credited back	-Shopify Payments: not returned-Third-party gateway: credited in proportion to the amount refunded

The table shows how a partial refund affects the order, but customers usually care more about what happens afterward. This process is explained later in the guide.

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2. When To Use A Partial Refund 

Understanding how partial refunds work is only the first step. Knowing why customers request them helps you prevent repeat issues and protect more revenue.

Partial refunds are common because not every problem requires a full return. In 2025, shoppers are expected to return about 15.8% of all retail purchases and 19.3% of online orders. Many of these cases can be resolved with a fair adjustment instead of refunding the entire order.

Here are the most common situations, along with practical refund amounts you can use as a starting point.

• Minor damage or defects: Common with fragile products like ceramics, glassware, and furniture, or apparel with printed or stitched details. 

• Shipping delays or the wrong shipping method: This is common for gifts, food, and other perishable products, and stores that offer express shipping. 
• Price drops and missed discount codes: This often happens in fashion, electronics, and stores that run frequent promotions. 
• Multi-item orders with a partial return: Easily found in beauty sets, apparel hauls, and bundle-heavy stores.

Handled well, a partial refund is more than a support cost. It can protect customer trust, support long-term conversion rate optimization, and increase the chance of another purchase.

How you resolve the issue often determines whether the customer shops with you again. Around 15% of checkout abandonment is linked to return-policy concerns, while Route reports that roughly 93% of shoppers review a store’s return policy before buying.

A quick, fair refund protects average order value over a customer’s lifetime, because the refund you give today often returns as the next order. Back it with a polished Shopify refund policy template so customers see clear terms before they buy. 

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3. How To Issue A Partial Refund On Shopify (Step By Step)

Issuing a partial refund takes a couple of minutes from your Shopify admin. This guide covers partial refunds. For a full refund walkthrough, see our guide to refunding an order on Shopify. 

Here is the flow. 

Step 1: Start your refund process

Go to Orders, click the order you want to refund, then click Refund at the top.

Step 2: Choose what to refund

On the refund screen, enter the quantity for each item you are refunding, and leave zero for the items not refunded.

In case you want to refund only part of an item’s cost, keep the quantity as is and edit the Refund amount field for a custom sum. 

Step 3: Add shipping and tax fees

• Shipping: in the Refund shipping section, select Shipping and enter the amount, up to what was charged.

• Duties and import taxes: this option shows only on orders that actually collected them, usually international orders. If you do not see it, the order had none. When it appears, choose whether to refund duties, import taxes, and customs clearance fees.
• Tax: there is no separate tax field to find. Shopify recalculates the tax on the refunded amount and includes it automatically.

Shipping and tax math trips up a lot of merchants, so in the next section, I’ll break down exactly how Shopify calculates both on a partial refund. 

Step 4: Add a reason and set the notification (optional)

Enter a Reason for the refund. This is only for internal management and is not shown to the customer.

The customer notification email is on by default. Leave it on unless you have a reason to turn it off.

Step 5: Finalize the refund

Review the details in the Summary panel carefully, as the refund cannot be reversed once it is issued.

If everything is correct, click Refund. The order status will then change to Partially refunded.

You can find the full steps in the Shopify Help Center guide to refunding orders.

Important: some third-party payment providers require partial refunds to be processed in their own dashboard. If so, issue the refund there and make sure the Shopify order record stays accurate. 

How Shopify calculates tax and the other refund fees

When you refund an item or part of an item, the tax tied to that amount is included in the refund automatically through the Shopify system. You do not need to work out the tax by hand, which keeps your reports clean.

• Duties and import taxes. If the order included duties or import taxes, usually on international orders, Shopify shows separate options to refund them. Select these only when they apply to the returned items.
• Discounts on the refund screen. Beyond tax, one more calculation catches Shopify merchants out. If you apply a discount to a line item on the refund page, it applies to that item’s full quantity, no matter how many units you are refunding. So watch this to avoid over-refunding a discounted item.

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4. What Happens After You Issue A Partial Refund

A partial refund does not end when you click Refund. Here is what changes on both sides.

#1 On the merchant side

• Payout: Shopify deducts the refund from your next available payout.
• Inventory: If you select the restock option, Shopify adds the refunded quantities back to your inventory.
• Transaction fees: With Shopify Payments, the original card processing fees are not returned. Your store absorbs both the refunded amount and the original processing fee.
• Chargebacks: The customer may still file a chargeback for the full order value after receiving a partial refund. Keep the refund record and Acquirer Reference Number as evidence.
• Reporting: Shopify automatically updates your sales reports and records the refund permanently in the order timeline.

#2 On the customer’s side

Customers usually want to know when and where their money will arrive. A refund can go to the original payment method, store credit, or a combination of both. The timing depends on the method:

• Credit card: Usually 5 to 10 business days
• Debit card: May arrive sooner, depending on the bank
• Store credit or gift card: Restored immediately
• Mixed payments: Shopify refunds the gift card portion first, then sends the remaining amount to the other payment method

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5. 3 Ways To Stop Refunds Before They Happen

Every partial refund solves a problem, but the better win is fewer problems to solve. Most avoidable refunds trace back to a handful of causes you can fix.

#1 Fix the root causes that trigger refunds

Refund reasons are valuable customer feedback. If “wrong size” appears repeatedly, your size chart or product details may be unclear. Track the reason for every refund, identify repeated patterns, and fix the underlying issue.

Focus on the three areas that cause many avoidable refunds:

• Product information: Add clear details on sizing, materials, dimensions, and limits, plus realistic photos from multiple angles.
• Packaging: Protect fragile items properly to reduce damage during delivery.
• Delivery expectations: Give honest shipping estimates, especially for gifts and time-sensitive orders.

Small improvements in these areas can prevent entire groups of refund requests.

#2 Resolve complaints without losing the sale

Speed and clarity decide whether a complaint ends in a refund or a relationship. Agree on the fix before you process anything. A short message like “I can refund $20 for the shipping delay, does that work for you?” prevents surprises and often settles the issue for less than a full refund.

To keep that consistent, give your team simple internal guidelines: 

• A set percentage for minor cosmetic damage
• A full shipping refund past a certain delay
• A price match within a set window

Clear rules build trust and speed up every reply, and they usually cost less than the alternative, since a small refund beats paying return shipping and losing the whole sale.

#3 Offer a gift to save the sale before a refund

Even after fixing the main causes of refunds, some problems will still happen. Your best chance to save the sale is before the customer submits a refund request.

Make it easy for customers to report an issue first. A thank-you card inside the package or a post-purchase email can encourage them to contact your support team if something goes wrong. For minor problems, consider offering a small incentive instead of a full cash refund. A gift with purchase, gift card, or store credit may resolve the issue at a lower cost while giving the customer a reason to shop with you again.

The challenge is delivering the right gift to one specific customer at the right moment. Shopify’s native Buy X Get Y discounts can target a customer segment, but the shopper still has to add the gift manually, and there is no built-in popup for choosing a reward. 

For a one-time recovery offer, these extra steps can weaken the surprise and make the gesture less effective. That gap is exactly what our own app, BOGOS, closes:

• You can add the recovery rewards to the cart automatically, including gifts, BOGO promotions, and discounted bundles. 
• Show a gift slider so the customer picks the reward they want, and limit the offer to that one buyer with customer tags, order history, location, or a private campaign link.

The unhappy customer gets a personalized surprise gift with no coding or manual steps, which rebuilds goodwill and turns a likely refund into another Shopify sale.

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Conclusion

A partial refund may be a small tool, but it can solve a complaint, protect most of the sale, and show the customer that your store is fair. Handled well, it can also increase the chance of another purchase.

Keep three points in mind. You can issue a partial refund from the Orders page in just a few steps. Shopify Payments does not return the original card processing fees, so include that cost in your decision. Finally, track every refund reason, because repeated issues show you what needs to be fixed.

You can also go beyond the refund itself. Pair a fast and fair resolution with a recovery offer, such as store credit, a discount, or a surprise gift on the next order. This turns a refund from a simple loss into an opportunity to rebuild trust, retain the customer, and support future Shopify sales. Shopify partial refund is one piece.

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