Sasquatch Apps

How to Add Fees for B2B and Wholesale Orders on Shopify

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Running a B2B or wholesale operation on Shopify is a different animal than selling direct-to-consumer. Your buyers are businesses — they expect net payment terms, want to pay by ACH or check, and often place large orders that come with their own set of billing complexities.

One of the most common pain points wholesale merchants face: how to properly charge fees on B2B orders without creating a mess of manual adjustments, awkward conversations, or lost margin.

This guide covers the wholesale fee problem in detail — and how tools like Canteen and Chargly help Shopify merchants handle it cleanly.

The B2B Fee Problem on Shopify

Most Shopify stores are set up for consumer checkout: a customer adds items to their cart, pays by credit card, and that’s it. B2B doesn’t work that way.

Here’s what makes wholesale fee collection complicated:

Payment Method Variation

Wholesale buyers often pay by ACH bank transfer, check, or wire — not credit card. But some do pay by card. And when a business pays a large invoice by credit card, the merchant’s processing fee can be significant. On a $10,000 wholesale order, a 2.9% processing fee is $290 coming out of your pocket.

Merchants in many US states can legally pass this surcharge back to the buyer — but setting it up properly on Shopify requires some thought.

Net Payment Terms

B2B orders frequently involve net-30, net-60, or even net-90 terms. That means the buyer places the order now and pays later. Shopify’s standard checkout flow isn’t designed for this — it expects payment at checkout.

Adding fees after the fact, once payment terms kick in, typically means manual order editing. That’s time-consuming and easy to miss.

Order Processing and Admin Fees

Some wholesalers charge a flat order processing fee, especially for small orders that don’t meet the minimum but are still fulfilled as a courtesy. Others charge a “small order fee” when buyers fall below a minimum order quantity. These are legitimate business charges, but Shopify has no native way to add them at checkout.

Custom Pricing Complexity

B2B buyers often get custom pricing — wholesale rates, tiered discounts, brand-specific catalogs. Layering fees on top of custom pricing adds another dimension of complexity that’s hard to manage manually.

Two Categories of B2B Fees

When it comes to wholesale fee collection, there are roughly two buckets:

1. Order-Level Fees (Flat or Percentage)

These are fees that apply to the order as a whole:

  • Small order / below-minimum fees — charged when an order doesn’t meet a minimum threshold
  • Processing or admin fees — a flat charge to cover order handling costs
  • Rush fees — charged when a buyer needs expedited fulfillment
  • ACH return fees — charged if an ACH payment fails

These fees are best handled at the order level, appearing as a clear line item so the buyer knows what they’re paying.

2. Payment Method Surcharges

These are fees that apply specifically because of how the buyer is paying:

  • Credit card surcharges — passing the processing cost back to the buyer when they pay by card
  • Wire transfer fees — covering the bank’s fee for incoming wire transfers

These fees are tied to the payment method selected, not the order itself.

How Canteen Handles B2B Order Fees

Canteen is built for exactly the kind of flat, named fees that wholesale operations need. Here’s how it helps:

Small Order Fees

If you have a minimum order amount (say, $250), and a buyer submits a $150 order, you might still fulfill it — but you want to charge a $25 small order fee to cover your costs.

With Canteen, you can create a fee that activates for orders below a certain cart value. The fee appears as a labeled line item at checkout, so the buyer sees it clearly and understands why it’s there.

Processing and Admin Fees

A flat $10 or $15 processing fee per wholesale order is common in many industries. Canteen lets you add a named, flat-amount fee that applies to all orders — or to specific order types, depending on your setup.

Rush and Handling Fees

If buyers can select expedited fulfillment, you can configure a corresponding fee that applies when that option is chosen. This ties the fee directly to the service being rendered.

Setting Up a B2B Order Fee with Canteen

  1. Install Canteen from the Shopify App Store
  2. Navigate to the fee builder in the Canteen dashboard
  3. Create a new fee and give it a clear name (e.g., “Small Order Processing Fee”)
  4. Set the fee amount — flat dollar amount or percentage of order value
  5. Configure conditions — such as minimum cart value thresholds
  6. Save and activate — the fee will appear at checkout for qualifying orders

Buyers see the fee name and amount before completing their order, which reduces disputes and maintains trust.

How Chargly Handles Credit Card Surcharges for B2B

When wholesale buyers pay by credit card — especially for large invoices — the processing fees add up fast. In states where surcharging is legal, merchants can pass the credit card processing cost back to the buyer.

Chargly is designed specifically for Shopify POS surcharging. For B2B merchants who process wholesale orders in person or via POS, Chargly automates the surcharge calculation and applies it at the point of sale.

When B2B Surcharging Makes Sense

  • High-ticket wholesale orders — even a 2-3% surcharge on a $5,000 order is a meaningful amount to recover
  • Mixed payment environments — some buyers pay by ACH (no fee), others by card (with surcharge); Chargly applies the fee only when applicable
  • POS-based wholesale transactions — trade shows, in-person wholesale showrooms, dealer counters

Surcharge Compliance for B2B

Credit card surcharges come with legal requirements:

  • Disclosure must happen before the transaction
  • Surcharge amounts are capped (typically at actual processing cost, not to exceed 3%)
  • Some states prohibit surcharging altogether

Chargly is built with these compliance requirements in mind. It handles the disclosure and calculation automatically, so you’re not improvising compliance on the fly.

Practical Setup Guide for Wholesale Fee Collection

Here’s a practical workflow for a typical wholesale Shopify operation:

Step 1: Map Your Fee Types

Before installing anything, list out every fee your business charges or wants to charge:

  • Processing fees
  • Small order fees
  • Rush/expedited fees
  • Credit card surcharges
  • Any government-mandated fees (environmental levies, etc.)

Step 2: Separate Order Fees from Payment Fees

This determines which app you need:

  • Order-level fees → Canteen
  • Credit card surcharges at POS → Chargly
  • Both → Install both

Step 3: Configure Canteen for Order Fees

Set up each fee type in Canteen with:

  • A clear, customer-facing name
  • The correct amount or percentage
  • Any conditions that trigger the fee (minimum order value, etc.)

Test with a sample order to confirm fees appear correctly at checkout.

Step 4: Configure Chargly for POS Surcharges

If you process wholesale orders at POS:

  • Install Chargly on your Shopify POS setup
  • Configure the surcharge percentage
  • Verify your state allows surcharging (Chargly’s documentation covers this)
  • Train your team on the disclosure requirement at point of sale

Step 5: Communicate with Your Buyers

B2B buyers appreciate transparency. Consider:

  • Adding a line item to your wholesale terms that mentions applicable fees
  • Including fee information in your onboarding email for new wholesale accounts
  • Listing fees clearly on your wholesale order page or portal

Surprises at checkout erode trust. Clarity builds it.

Common Questions from Wholesale Merchants

Can I add a fee only for orders under a certain minimum?

Yes — Canteen supports conditional fees based on cart value. You can set a minimum threshold below which the fee activates.

Can I waive the fee for specific customers?

This depends on how your store is set up. For wholesale portals with customer-specific pricing, you can typically structure things so certain customer segments don’t see the fee. Discuss your specific setup with the Canteen support team.

Is a credit card surcharge the same as a service fee?

Not exactly — though they’re related. A credit card surcharge is specifically tied to the cost of processing a card payment. A service fee is a broader charge for services rendered. The distinction matters legally. See our guide to service fees at Shopify POS for more on this.

What about net terms — can I add fees for late payment?

Late payment fees are handled differently — they’re typically added to invoices outside of Shopify’s checkout flow. Canteen focuses on fees added at checkout time; late fees are better handled through your invoicing system.

The Bigger Picture: Protecting Your Margins on Wholesale

B2B merchants often operate on thinner margins than DTC brands. Every avoidable cost — unreimbursed credit card fees, admin overhead from manual adjustments, fees you forget to charge — eats into profitability.

Getting your fee collection dialed in isn’t just a compliance exercise. It’s a margin protection strategy. When your systems collect the right fees automatically, you’re not leaving money on the table with every wholesale order.

Ready to clean up your B2B fee collection?

  • Install Canteen to add order-level fees and processing charges at wholesale checkout
  • Install Chargly to handle credit card surcharges at Shopify POS