Sellerboard For Shopify - Payment Fees Tutorial - Organize Payment Fees From Payment Providers

Sellerboard for Shopify helps merchants include payment-processing and gateway costs in profitability instead of treating every dollar of revenue as profit.

Sellerboard for Shopify can track payment fees, product costs, shipping, advertising, discounts, returns, pick-and-pack costs, and other expenses in one reporting system.

The Payment Fees section is important because Shopify stores can accept payments through several methods with different percentage rates, fixed charges, Shopify transaction fees, negotiated pricing, currency costs, and refund rules.

When the rates inside Sellerboard do not match the real processor agreement, the dashboard can overstate or understate profit.

The correct setup maps every active gateway to the fees that actually apply to the store and then reconciles the estimate with payout reports and processor statements.

This guide explains every main field, Shopify Payments versus third-party gateways, percentage and fixed-fee calculations, refunds, disputes, reconciliation, and common reporting mistakes.

What Are Shopify Payment Fees?

Shopify payment fees are the costs generated when a customer pays for an order.

The total can include a processing percentage, a fixed per-transaction charge, an additional Shopify transaction fee, currency conversion, cross-border costs, installment charges, disputes, and other provider-specific fees.

Do not assume that one rate applies to every order.

Actual fees can differ by plan, country, card type, currency, capture method, payment method, and negotiated terms.

Why Payment Fees Matter For Profitability

A small missing fee can create a large monthly reporting error when sales volume grows.

The error becomes larger when fixed fees, refunds, chargebacks, and currency costs are also missing.

Accurate payment-fee tracking helps compare channels, products, order values, and payment methods using real contribution profit.

How To Open The Payment Fees Dashboard

• Sign in to Sellerboard for Shopify.

• Select the correct connected Shopify account.

• Open Payment Fees from the left navigation.

• Review every gateway, marketplace source, and payment method shown.

• Compare each default with the real provider agreement and Shopify settings.

• Edit the percentage and fixed values when they differ.

• Save the changes and review recalculated profit.

• Reconcile several real orders before relying on the dashboard.

Different stores can have different plans, countries, currencies, providers, and negotiated rates.

Record the effective date of every rate change so historical reporting can be investigated correctly.

The Main Sellerboard Payment Fee Fields

Sellerboard can preload common values, but a default is only a starting point.

Use Shopify settings, provider pricing, invoices, payout reports, and negotiated contracts as the source of truth.

Shopify Payments Vs Third-Party Providers

Shopify Payments is Shopify's built-in processing option in supported countries and regions.

A third-party provider is an external processor used instead of or alongside Shopify Payments.

The cost structure can differ significantly.

Avoid double counting when a cost is imported through another Sellerboard expense source.

Test at least one real order from every major payment method.

How Shopify Payments Fees Work

Shopify Payments rates depend on the store country, Shopify plan, transaction type, and payment method.

The fee can include a percentage plus a fixed amount for an online transaction.

Review the official Shopify Payments guide and the rates shown inside the store account.

• Confirm the Shopify plan.

• Confirm the store country and settlement currency.

• Check online and in-person rates separately.

• Review premium-card, international, installment, and currency terms.

• Confirm whether manual capture changes the rate.

• Check the current refund-fee treatment.

• Compare the configured rate with a real payout.

Do not copy an old US example into a different country or plan.

How Third-Party Gateway Fees Work

A third-party gateway can create two percentage charges.

The processor may charge its own rate, while Shopify may charge an additional transaction fee based on the plan and payment setup.

The provider may also charge a fixed amount.

• Enter the applicable Shopify transaction percentage in Shopify fee.

• Enter the provider percentage in Gateway fee.

• Enter the fixed amount in Gateway fixed fee.

• Add cross-border, currency, installment, or risk fees through the appropriate expense method.

• Check whether refunds return the percentage fee, fixed fee, neither, or part of the cost.

• Track chargeback and dispute fees when they are not included automatically.

Do not enter the combined percentage into both fields because that doubles the estimated expense.

Payment Fee Formula

Confirm which transaction amount the provider uses because the base can include shipping, tax, tips, or other payment components.

The correct formula should be tested against the processor statement.

Worked Example With A Third-Party Gateway

Assume a customer pays $100.

Assume Shopify charges a 1% third-party transaction fee and the processor charges 2.9% plus $0.30.

The remaining $95.80 is not profit because product cost, fulfillment, shipping, advertising, returns, discounts, and overhead still need to be deducted.

The example is educational and should not be copied as the current rate for a real store.

Why Fixed Fees Matter More On Small Orders

A store with a low average order value can lose more margin to fixed charges than a percentage-only review suggests.

Use order-level calculations when order values vary significantly.

Automatic Capture Vs Manual Capture

Some payment arrangements use different commercial rates depending on how the payment is captured.

• Check the payment-capture setting in Shopify.

• Confirm whether orders are captured automatically or manually.

• Review the rate shown in the provider agreement.

• Use the Sellerboard row that matches the actual configuration.

• Test a real order after changing capture settings.

A settings change can make an older Sellerboard rate inaccurate even when the provider name remains the same.

Refunds And Payment Fees

A refund does not always reverse every original payment cost.

The percentage fee, fixed fee, Shopify transaction fee, currency cost, and refund processing treatment can differ by provider and country.

• Review the provider's current refund policy.

• Check whether the fixed fee is retained.

• Check whether Shopify returns any additional transaction fee.

• Confirm how partial refunds are handled.

• Compare the refund in Shopify, the processor statement, and Sellerboard.

• Add missing retained costs through the correct Sellerboard expense category.

Do not assume that a fully refunded customer order produces zero payment-processing expense.

Chargebacks And Disputes

Chargebacks can create a disputed order amount, a separate fee, operational work, and a delayed payout.

A Payment Fees row may not represent every dispute cost.

• Track the chargeback fee.

• Track the lost product and fulfillment cost when applicable.

• Track whether the original processing fee remains.

• Record recovered funds when the dispute is won.

• Separate fraud, service, fulfillment, and product-quality causes.

Use Sellerboard indirect expenses or another supported cost method when the charge is not imported automatically.

Currency Conversion And International Fees

Cross-border ecommerce can add currency conversion, international card, settlement, bank, and provider costs.

These charges may appear outside the normal percentage and fixed-fee fields.

• Confirm the presentment currency paid by the customer.

• Confirm the store and payout currencies.

• Review the conversion rate and conversion fee.

• Check international-card or cross-border surcharges.

• Review bank or payout-account costs.

• Allocate material currency costs to the correct reporting period.

A store can appear profitable in sales currency while losing margin during settlement.

Reconcile Sellerboard With Real Payouts

Configuration is complete only after Sellerboard agrees reasonably with actual statements.

• Choose several orders from each major gateway.

• Record the customer payment amount.

• Record the Shopify transaction fee when applicable.

• Record the processor percentage and fixed charge.

• Check refunds, currency costs, disputes, and adjustments.

• Compare the total with Sellerboard.

• Investigate every recurring difference.

• Update the rate or additional expense rule.

A small rounding difference can be normal.

A repeating percentage or fixed difference usually indicates a missing or incorrect setting.

Payment Fees Are Only One Profitability Layer

Accurate payment fees do not make the dashboard accurate when other costs are missing.

My Sellerboard for Shopify shipping-cost tutorial explains the shipping layer.

My Sellerboard pick-and-pack tutorial covers fulfillment handling.

My Sellerboard indirect-expenses tutorial explains costs not tied directly to one order.

How To Audit Payment Fees Monthly

• Export or open the payment-provider statement.

• Compare total processed sales with Shopify and Sellerboard.

• Calculate the provider's effective fee rate.

• Review the largest gateway differences.

• Check new payment methods and removed gateways.

• Review refunds, disputes, currency costs, and adjustments.

• Confirm the Shopify plan and provider contract have not changed.

• Document any Sellerboard rate update and effective date.

A monthly audit catches silent fee changes before they distort several months of product decisions.

Common Payment Fee Setup Mistakes

• Using one rate for every payment method.

• Ignoring fixed per-transaction charges.

• Omitting Shopify's additional third-party transaction fee.

• Charging a Shopify fee when Shopify Payments makes it inapplicable.

• Entering the combined percentage in both percentage fields.

• Using an outdated public rate.

• Ignoring negotiated or country-specific pricing.

• Assuming refunds reverse every original fee.

• Ignoring chargebacks and currency conversion.

• Failing to reconcile with real payouts.

• Counting the same fee in Payment Fees and another expense category.

Sellerboard For Shopify Vs Sellerboard For Amazon

The platforms solve similar profitability problems but use different data structures and fee logic.

Sellers operating both channels should use the correct extended trial for each account.

Who Should Use The Shopify Payment Fees Dashboard?

• Stores using more than one payment provider.

• Stores with meaningful monthly payment-processing costs.

• Businesses using external gateways with additional Shopify fees.

• Stores selling internationally or in several currencies.

• Businesses with low average order values where fixed fees matter.

• Teams comparing product, channel, and gateway profitability.

A very small store can calculate fees manually, but the dashboard becomes more valuable as order volume and payment complexity grow.

Frequently Asked Questions

What Should I Enter In Shopify Fee?

Enter the additional Shopify transaction percentage that applies to the gateway and store plan.

Use zero when the fee does not apply, but verify the current Shopify setup first.

What Should I Enter In Gateway Fee?

Enter the payment provider's percentage charge for the relevant transaction type.

What Is Gateway Fixed Fee?

It is the fixed amount charged per eligible payment, such as a per-transaction amount added to the percentage fee.

Does Shopify Payments Have A Transaction Fee?

Shopify Payments has processing costs, but Shopify states that third-party transaction fees are not charged for orders processed through Shopify Payments and certain supported methods.

Verify the current country, plan, and method rules.

Can Different Gateways Have Different Rates?

Yes, each provider and payment method can have different percentage, fixed, international, refund, and dispute costs.

Does Sellerboard Import Every Payment Fee Automatically?

Sellerboard can import and calculate supported data, but the merchant should verify defaults and add missing provider-specific costs when necessary.

How Often Should I Check The Rates?

Review them after changing the Shopify plan, payment provider, country, currency, contract, capture method, or payment methods.

A monthly reconciliation is useful for active stores.

How Do Refunds Affect Payment Fees?

The effect depends on the provider and region because some fees may be retained or only partly reversed.

Should Chargeback Fees Be Added Separately?

Add them separately when they are not already imported or included in the Payment Fees calculation.

Is The Two-Month Trial Available For Shopify And Amazon?

The supplied links provide separate extended offers for Sellerboard for Shopify and Sellerboard for Amazon.

Open the correct link for the store or marketplace you want to connect.

Final Thoughts

Payment fees are unavoidable, but hidden or incorrectly configured fees do not need to distort Shopify profit.

Open Sellerboard's Payment Fees section and map each active payment method to the actual Shopify percentage, provider percentage, and fixed charge.

Then test the calculation against real payouts, refunds, disputes, and currency adjustments.

Do not stop after configuring payment fees because COGS, shipping, advertising, pick and pack, returns, and overhead also affect contribution profit.

Use the Sellerboard for Shopify two-month offer to validate the setup with real store data.

Use the separate Sellerboard for Amazon offer when you need Amazon-specific profitability and operations reporting.