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Shopify fee audit guide

How to audit Shopify fees after partial refunds

A fee can be collected correctly at checkout and still become difficult to reconcile after a discount, partial refund, or full merchandise refund. This guide provides a practical way to compare what should have happened with what appears in the completed order.

Merchant checklist About 8 minutes Updated July 2026
Scope of this guide: This is an operational reconciliation checklist. It does not determine whether a fee is lawful, properly disclosed, taxable, or permitted by a payment network. Review those questions separately with qualified legal, tax, and payment professionals.

Why refunds create confusion

Most merchants think about a fee when it is first added to the cart. The harder question comes later: what should happen when only part of the merchandise is refunded?

Depending on the fee app and store setup, the fee may appear as a separate line item. If that line represents the entire fee as a quantity of one, the standard refund screen may offer only two obvious choices: refund the whole fee or leave it in place. A proportional adjustment may require a separate calculation or manual review.

That does not automatically mean something is wrong. The audit begins by defining the merchant's intended policy, then checking whether completed orders follow it consistently.

Choose the intended fee policy

Pick the rule that should apply before reviewing any orders. Otherwise, the audit can mistake a policy choice for an error.

Policy 1

Keep the fee on partial refunds

The original fee remains unchanged unless all merchandise is refunded. This is often the easiest policy to operate consistently.

Policy 2

Refund the full fee after any refund

Any merchandise refund triggers a complete fee refund. This is simple to recognize but may refund more than a proportional rule.

Policy 3

Adjust the fee proportionally

The remaining fee should match the merchandise value left on the order. This requires a clear formula and may need manual handling.

Write the policy down. Include who owns the decision, which fee rules it covers, and whether discounts, taxes, shipping, or other fees belong in the calculation base.

Run a manual audit

  1. Define which orders were eligible

    Identify the products, customers, locations, payment methods, or order values that should trigger the fee. An order that was never eligible should not be counted as a missing-fee problem.

  2. Confirm the intended calculation base

    Use the merchandise amount the rule is supposed to cover. Do not accidentally calculate a percentage from a subtotal that already includes the fee itself.

  3. Record the original fee

    Note the fee description, amount, and whether it appeared once, more than once, or not at all. Keep the evidence tied to the order number and date.

  4. Separate merchandise refunds from fee refunds

    Review the refund lines individually. A merchandise refund and a fee refund may be recorded as separate events even when they were processed together.

  5. Calculate the fee that should remain

    Apply the written refund policy to the merchandise value left on the order. Round consistently with the original fee rule.

  6. Classify the result

    Mark the order as correct, missing fee, duplicate fee, incorrect amount, unexpected fee refund, unexpected fee retention, or manual review required.

Work through a simple example

A customer buys two $100 items. The store adds a 2.5% fee based on the $200 merchandise total, so the original fee is $5. One $100 item is later refunded.

Merchant policy Expected fee after refund What to verify
Keep fee on partial refunds $5.00 No fee refund was issued.
Refund full fee after any refund $0.00 The entire $5 fee was refunded.
Proportional adjustment $2.50 The order received a $2.50 fee adjustment or equivalent credit.

The same order can be correct under one policy and incorrect under another. That is why the written policy comes first.

Warning signs worth investigating

Missing fee

An eligible order has no recognizable fee line or the fee amount is zero when it should not be.

Duplicate fee

The same fee appears more than once, or multiple fee lines produce a total above the intended amount.

Wrong calculation base

The percentage appears to include the fee itself, excluded items, shipping, taxes, or another amount outside the written rule.

Unexpected discount interaction

The fee changes when a discount is applied even though the merchant intended the fee to use the pre-discount or post-discount value.

Fee remains after a full merchandise refund

All merchandise has been refunded, but the fee remains collected despite a policy that requires a full fee refund.

Inconsistent outcomes

Similar orders follow different fee or refund patterns without a clear rule explaining the difference.

Document the result

A useful audit record should make it possible for another person to understand the finding without opening technical logs.

Order reference
Order number and relevant dates
Expected rule
Fee rate or fixed amount, eligibility, and refund policy
Observed outcome
Original fee, merchandise refunds, and fee refunds
Estimated impact
Amount missing, duplicated, retained, or refunded unexpectedly
Recommended check
Merchant action, app-setting review, or manual follow-up
Avoid placing customer names, addresses, payment details, credentials, or API keys in the audit record unless they are genuinely required and protected through an approved process.

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Shopify is a trademark of Shopify Inc. ReadyCheck Labs is not affiliated with or endorsed by Shopify Inc. This guide is not legal, tax, payment network, or accounting advice.