Overcoming Payment  Challenges in B2B Wholesale with Shopify

B2B wholesale businesses often struggle with high transaction fees, chargebacks, and payment holds. Leveraging Shopify’s solutions, Shopify apps, and strategic payment methods can help reduce costs, mitigate risks, and ensure smooth transactions.

Payment Processing Fees Challenges

Cross-Border Fees & Currency Conversion Issues

Processing payments in multiple currencies leads to hidden costs.

Use Case: A European electronics supplier is charged extra when converting USD payments to EUR, reducing profit margins.

Solution:

Shopify Default Solution

• Use Shopify Payments’ multi-currency support to accept payments in different currencies without extra conversion fees.
• Enable automatic currency conversion based on the customer’s location, ensuring localized pricing.
• Adjust product pricing per currency using Shopify Markets, maintaining profit margins across regions.
• Use Shopify’s payout accounts to receive funds in supported currencies and minimize conversion costs.

Manual Solution

• Open multi-currency bank accounts (e.g., with Wise or Revolut) to receive funds in different currencies without automatic conversions.
• Manually set product prices for different regions in Shopify’s pricing settings.
• Use third-party payment gateways that offer better exchange rates for non-Shopify Payments transactions.
• Monitor currency fluctuations and adjust pricing manually to maintain profitability.

Shopify Apps Solution

To overcome payment processing fees and currency conversion challenges, Shopify apps can be utilized for automation and better cost management. There are many cross-border currency conversion apps available in the Shopify App Store that help merchants:

• Automatically display local currency prices based on customer location or selected currency.
• Reduce conversion fees by allowing payments in multiple currencies.
• Sync real-time exchange rates to maintain accurate pricing.
• Offer localized checkout experiences to improve customer trust.

You can explore these apps in the Shopify App Store using the link below:

Link: Shopify App Store – Currency Conversion Apps

Chargeback Risks & Disputes

Large B2B orders face chargebacks due to fraudulent claims or disputes.

Use Case: A tech accessories wholesaler receives a chargeback from a retailer claiming non-receipt, despite delivery confirmation.

Shopify Default Solution

• Shopify Protect (U.S. only) – Covers fraudulent chargebacks on eligible orders for merchants using Shopify Payments.
• Fraud Analysis Tools – Shopify automatically flags high-risk transactions and provides fraud indicators.
• Shopify Flow (for Plus users) – Automates fraud detection by setting up rules to cancel suspicious orders.

 Manual / Process-Based Solution

• Encourage Secure Payment Methods – Prioritize wire transfers or ACH payments instead of credit cards to minimize chargeback risks.
• Manually Review Orders – Check for mismatched billing and shipping addresses, large orders from new customers, or unusual purchase patterns.
• Require Identity Verification – Request business licenses or proof of authorization for high-value wholesale orders.

Shopify Apps Solution

There are several Shopify apps available to help minimize chargeback risks and enhance payment security. These apps provide features such as fraud detection, secure payment processing, and automated chargeback management.

You can explore and choose the most suitable app for your business needs by visiting the Store: Shopify App Store – Chargeback Protection

High Transaction Costs

Wholesale orders are large, and payment gateway fees cut into margins.
Use Case: A fashion distributor selling bulk apparel struggles with high PayPal fees and looks for alternatives like ACH transfers.

Solutions to Reduce Transaction Costs

Shopify Default Solution

• Shopify Payments – Offers lower transaction fees compared to third-party gateways.
• Negotiated Rates for Shopify Plus – Shopify Plus merchants can negotiate better credit card processing rates, further reducing costs.

 Manual / Process-Based Solution

• Use Alternative Payment Methods – Many B2B wholesalers prefer wire transfers, ACH payments, or checks to avoid high gateway fees.
•  Manual Payment Tracking – Requires matching transaction IDs with order IDs to ensure seamless reconciliation, adding an administrative burden.

Shopify Embedded Solution (Best for Automation)

Custom Shopify Embedded App that enables you to automatically add payment transaction fees directly to customer payments.

• Automatically include payment transaction fees in the total amount.
• Ensure transparent cost calculation for B2B wholesale transactions.
• Streamline payment processing without manual adjustments.

Shopify Embedded App provides a fully automated and tailored experience for your B2B wholesale business.

Payment Gateway Holds on Large Transactions

Some providers flag high-value orders as suspicious, delaying fund availability.
  Use Case: A furniture wholesaler has their $15,000 transaction held by Stripe for review, delaying order fulfillment

Shopify Default Solution

• Use Shopify Payments – Shopify Payments offers predictable payout schedules with a lower risk of unexpected holds compared to third-party processors.
• Enable Manual Payment Methods – Shopify allows businesses to accept bank deposits, cash on delivery (COD), or external invoicing, reducing reliance on gateways prone to holding funds.

Manual / Process-Based Solution

• Prefer ACH Transfers or Wire Payments – Bypasses payment gateway holds entirely, ensuring immediate access to funds.
• Maintain a Strong Transaction History – Establish trust with payment providers by maintaining consistent transaction patterns and proper documentation for large orders.
• Communicate with Payment Providers – Notify your payment processor in advance about high-value transactions to prevent unnecessary delays.

 Shopify Apps Solution

• There are several apps available that help businesses manage large transactions, prevent payment holds, and facilitate alternative payment methods.
• You can explore high-value transaction-friendly payment processors and invoicing solutions via the Shopify App Store:

High-Risk Business Classification

Certain industries (CBD, supplements, electronics) face higher fees or denial from some payment processors.

Use Case: A CBD product wholesaler struggles to find a payment gateway willing to process their transactions.

Shopify Default Solution

• Limited Payment Gateway Support – Shopify Payments does not support high-risk industries like CBD, supplements, and certain electronics.
• Third-Party Payment Gateways – Shopify allows integration with high-risk-friendly processors such as Authorize.net, Pinwheel, and Square (if available for the business type and location).
• Manual Payment Methods – Shopify enables manual payment options like bank deposits, cash on delivery (COD), or external invoicing, reducing reliance on traditional processors.

 Manual / Process-Based Solution

• Secure a High-Risk Merchant Account – Work with banks and financial institutions that cater to high-risk businesses, reducing the risk of sudden account freezes.
• Diversify Payment Options – Offer ACH transfers, wire payments, and cryptocurrency to minimize dependency on high-risk credit card processors.
• Maintain Compliance & Transparency – Clearly outline refund policies, terms of service, and product legality to build trust and reduce disputes.
• Proactive Chargeback Prevention – Use strict fraud screening and require additional verification (e.g., business licenses) for wholesale buyers.

Shopify Apps Solution

• There are several Shopify apps that cater to high-risk payment processing, chargeback prevention, and alternative payment solutions.
• You can explore specialized high-risk payment processors and fraud protection apps via the Shopify App Store: High-Risk Payment Solutions

Recommendations for Overcoming Payment Processing Challenges

Navigating payment challenges is essential for B2B wholesale success. Here are key strategies to optimize payment processing:

• Use Shopify Payments (if applicable) – Benefit from predictable payouts and lower processing risks.
• Diversify Payment Methods – Offer ACH, wire transfers, or manual payments to reduce gateway fees and fund holds.
• Choose High-Risk-Friendly Payment Providers – If in a restricted industry, use specialized merchant accounts.
• Implement Fraud Prevention Measures – Utilize Shopify’s fraud tools or third-party apps to reduce chargebacks.
• Plan for Multi-Currency Transactions – Use cross-border payment solutions to minimize conversion fees.
• Monitor & reduce Fees – Regularly review processing costs and negotiate better rates with providers.

By adopting these strategies, wholesalers can reduce costs, minimize risks, and streamline transactions, ensuring long-term growth and customer trust in the competitive B2B market.

2. Implementing Payment Restrictions(Hide) Challenges

Hiding Payment Methods

Shopify lacks built-in features to restrict payment options by customer group.

Use Case: A B2B supplier wants wholesale buyers to pay only via bank transfer but cannot disable credit card payments for them.

Shopify Default Solution (Limited Customization)

• Shopify does not provide built-in options to restrict payment methods based on customer groups.
• However, merchants can set up manual payment methods (e.g., bank transfer, COD) and specify in checkout instructions that they are for wholesale customers only.
• Shopify Plus users can use Shopify Scripts (if applicable) to customize checkout logic.

 Customization-Based Solution

• Tag Wholesale Customers – Assign tags like “Wholesale” or “B2B” to customers in Shopify Admin.
• Provide Payment Instructions – Display bank transfer or wire payment details in the order confirmation email for tagged customers.

Shopify Apps Solution (Best for Automation)

• A custom Shopify Embedded App that allows you to control payment options based on customer groups seamlessly.
• With this solution, you can:
  Create customer groups using Shopify’s customer tagging system.
  Assign customers to specific groups (e.g., Wholesale, Retail).
  Dynamically show or hide payment methods based on predefined customer rules.
• Shopify Embedded App ensures a fully automated and tailored experience for your B2B wholesale business.

Fraud Risks from Unrestricted Payments

Allowing all payment methods increases the risk of fraudulent transactions.

Use Case: A beverage wholesaler gets multiple fraudulent credit card orders from unknown buyers in high-risk regions.

Shopify’s Built-in Fraud Prevention Solution

• Fraud Analysis – Flags high-risk orders and provides fraud indicators.
• Shopify Payments Protection (if using Shopify Payments) – Includes:
  • Chargeback protection
  • 3D Secure authentication
  • CVV/AVS verification
• Manual Payment Capture – Allows reviewing and capturing payments manually instead of auto-processing.
• Restrict High-Risk Regions – Block specific countries/regions from checkout via shipping settings.
• Shopify Flow (Shopify Plus only) – Automates fraud prevention, such as holding or canceling high-risk orders

Fraud Prevention Solutions Using Liquid in Shopify

High Priority (Critical Fraud Prevention)

• Block checkout for high-risk countries – Restrict purchases from specific countries.
• Disable checkout for mismatched billing & shipping addresses – Prevent fraudulent transactions.
• Restrict guest checkout for high-risk products – Require account creation before purchase.
• Hide COD for first-time buyers – Prevent fake orders via Cash on Delivery.
• Prevent checkout from disposable email domains – Block temp/fraudulent emails.
• Limit high-value orders for new customers – Require verification for expensive orders.
• Detect and restrict proxy/VPN users – Block users hiding their location.
• Block checkout if the customer’s IP doesn’t match billing country – Prevent mismatched fraud.
• Prevent multiple failed payment attempts – Limit retries on stolen cards.
• Auto-cancel orders from known fraudulent users – Ban repeat offenders.

Medium Priority (Additional Security Layers)

• Block orders with blacklisted ZIP codes – Flag high-risk locations.
• Limit maximum order quantity for high-risk products – Prevent bulk fraud.
• Delay order confirmation for high-risk payments – Review before processing.
• Restrict checkout for newly created accounts – Prevent scammers using fresh accounts.
• Disable checkout during unusual traffic spikes – Stop bot attacks.
• Show CAPTCHA for high-risk customers – Add extra verification.
• Require phone verification for expensive orders – Reduce fraud risk.
• Block orders containing suspicious keywords in addresses – Detect fake inputs.
• Restrict multiple orders from the same email in a short time – Prevent card testing.
• Warn customers before checking out high-risk products – Inform about security concerns.

Low Priority (User Behavior & Experience Enhancements)

• Restrict bulk purchases from a single IP – Limit non-trusted buyers.
• Disable discounts for high-risk customers – Prevent abuse of promo codes.
• Prevent orders from overly long or fake names – Stop auto-generated names.
• Require additional approval for risky payment methods – Hold for review.
• Block purchases made at unusual hours (e.g., midnight orders) – Detect suspicious activity.
• Prevent orders using copy-paste email addresses – Reduce bot abuse.
• Show “Limited Stock” message to deter bulk fraud – Discourage fake bulk orders.

Shopify Embedded App Solutions for Fraud Prevention

In addition to liquid customizations and third-party apps, a Shopify-embedded app can provide dynamic fraud prevention features. Here’s how:

Hide Payment Methods Based on Customer Location

• Use Shopify’s API to detect the customer’s IP address or billing/shipping country.
• Dynamically disable or hide specific payment methods for high-risk locations.

Example: If a customer is from a high-risk country, disable Cash on Delivery (COD) or Bank Transfers.

Regulatory Compliance Issues

Some industries require KYC (Know Your Customer) verification before processing payments.

Use Case: A medical equipment supplier must verify buyers before allowing purchases but lacks an automated solution on Shopify.

Shopify default solution:

• Manual Payment Capture – Approve payments manually before charging customers (Settings > Payments).
• Customer Accounts Requirement – Allow only registered customers to make purchases (Settings > Customer Accounts).
• Order Notes for Verification – Enable order notes at checkout for customers to provide necessary details.
• Draft Orders for Verification – Collect customer details first, verify manually, then send a payment invoice.
• Restrict Checkout Access – Use Shopify Plus B2B features to allow purchases only from approved customers.
• Customer Tags for Verification – Tag verified customers and allow only them to place orders (Shopify Plus needed).
• Checkout Scripts (Shopify Plus) – Block purchases unless a customer meets certain verification criteria.
• Manual Fulfillment Hold – Prevent auto-fulfillment until orders are reviewed and verified.
• Verification via Shopify Forms – Use Shopify’s contact form to collect verification details before allowing purchases.
• Quote-Based Orders – Replace direct checkout with a request-a-quote system using Shopify’s Draft Orders.
• Mandatory Agreement Checkbox – Add a required checkbox at checkout for customers to confirm compliance with verification requirements.

Custom liquid-based solution :

High Priority (Core Compliance & Checkout Control)

• Restrict Checkout Access – Block checkout for unverified users using customer tags.
• Require Document Upload Before Checkout – Add a file upload field for ID verification in the cart.
• Hide Prices & Add to Cart for Unverified Users – Display pricing and purchase options only for verified customers.
• Redirect Unverified Users to a Verification Page – Automatically send them to a separate KYC form before checkout.
• Block Purchase of Restricted Products – Prevent adding specific items to the cart unless verified.
• Disable Guest Checkout for KYC-Required Products – Force customers to log in and verify before purchasing.
• Require Additional Information at Checkout – Collect license numbers or other credentials via checkout attributes (Shopify Plus).
• Prevent Checkout for Orders Containing Certain Tags – Check cart item tags and block checkout if any restricted items are in the cart.
• Disable One-Click Checkout for Unverified Users – Hide express checkout options (Shop Pay, Apple Pay) unless verified.

Medium Priority (Fraud Prevention & Verification Enhancements)

• Auto-Tag Customers Based on Registration Input – Apply “Verified” tags after manual review of registration data.
• Lock Specific Collections for Verified Customers Only – Hide restricted product categories from unapproved users.
• Show a Verification Warning on Product Pages – Alert users that an item requires approval before purchase.
• Limit Bulk Purchases for Unverified Users – Restrict quantity per order to prevent unauthorized reselling.
• Display Different Payment Methods Based on Verification – Allow only secure payment methods for unverified users.
• Delay Order Confirmation for Unverified Customers – Prevent instant fulfillment until manual review is complete.
• Block Checkout Based on Customer Email Domain – Restrict orders from personal or disposable email providers.
• Add a Custom Verification Form on the Account Page – Allow users to submit verification documents via their profile.
• Show Different Product Descriptions Based on Verification – Change product details for unverified vs. verified customers.
• Auto-Cancel Orders if Verification Isn’t Completed in X Hours – Use a script to cancel unpaid orders if KYC isn’t done.
• Restrict Payment Methods for High-Value Orders – Block PayPal/Credit Card for large orders unless verified.

Low Priority (User Experience & Awareness)

• Require Age Verification Before Checkout – Ask users to confirm they meet age requirements.
• Show a Countdown Timer for Manual Verification – Display estimated verification time after order submission.
• Custom Pop-Up Alerts for KYC Verification – Warn users that verification is required before checkout.
• Restrict Checkout by Customer’s Country – Block certain locations unless verified.
• Use Draft Orders Instead of Checkout – Convert orders into draft status for manual review.
• Add an “Account Pending Approval” Message – Display a banner on the account page if verification is in progress.
• Prevent Account Creation with Fake or Generic Names – Block registrations with common fake names or placeholders.
• Show Estimated Approval Time on Checkout Page – Inform customers of expected KYC processing time.
• Disable Discount Codes for Unverified Customers – Only allow promo codes for verified buyers.
• Restrict Access to Certain Pages Until Verified – Hide specific pages like “Wholesale Pricing” for unverified users.

Shopify App Solutions: 

There are several apps available that provide solutions for regulatory compliance payment issues. You can explore them using the following

link: Shopify App Store

Let me know if you need any recommendations or assistance in selecting the right app for your needs.

Country-Specific Payment Restrictions

Shopify doesn’t allow businesses to block payment methods based on customer location.

Use Case: A US-based company wants to prevent international buyers from using PayPal due to higher fees, but can’t configure this natively.

Native Shopify solutions:

• Use manual payment methods to offer PayPal only for specific countries with instructions.
• Disable PayPal entirely and handle selective access via draft orders or email invoices.
• Create country-specific shipping zones and add payment guidance in shipping descriptions.
• Add cart or product page messages to inform international customers not to use PayPal.
• Use Shopify Markets with region-specific domains to guide users through different flows.
• Run separate Shopify stores per region to enable/disable payment methods independently.
• If on Shopify Plus, use Shopify Functions to conditionally hide/show payment methods by country.

Consolidated Solutions to Restrict Payment Methods by Country/Region in Shopify Using Liquid & Native Features

Shopify App Solutions:

There are several apps available that provide solutions for challenges with country/region-specific payment restrictions. You can explore them using the following

link: Shopify Apps Store

Let me know if you need any recommendations or assistance in selecting the right app for your needs.

Customer-based payment restrictions

Some buyers prefer credit cards, while businesses prefer ACH or wire transfers.

Use Case: A retailer insists on paying via PayPal, but the wholesaler prefers ACH to avoid high transaction fees.

Shopify Native solution:

• Tag customers as Retail or Wholesale in the Shopify admin.
• Enable manual payment methods (ACH, Wire Transfer) in Settings > Payments.
• Retail customers check out normally using PayPal or a credit card.
• For wholesale clients, create a Draft Order and select ACH or Wire as payment.
• Send wholesale clients the draft invoice to bypass PayPal and credit card options.
• Shopify can’t restrict payment methods per customer type at standard checkout.
• Use manual processes and customer tagging to manage payment preferences.

Custom Liquid Solutions

• Cart Message for Wholesale Customers
  Show a message in the cart guiding wholesale users to use ACH instead of PayPal.
• Redirect Wholesale Clients After Login
  Auto-redirect tagged users to a page with payment instructions after login.
• Hide Checkout Button for Wholesale Customers
  Hide or disable the checkout button on the cart for wholesale clients and show an invoice request link.
• Pre-fill Invoice Request Forms
  Auto-fill customer name/email in invoice request forms using Liquid and JavaScript.
• Custom Wholesale Checkout Page
  Create a dedicated page with bank details, shown only to wholesale customers.
• Conditional Product or Cart Banners
  Display ACH/Wire-only banners on product/cart pages for wholesale clients.
• Theme Duplication for Customer Groups
  Maintain separate themes for retail and wholesale experiences, with custom messages and styling.
• Draft Order Flow with Manual Payment Methods (from native workflow)
  Wholesale clients bypass regular checkout by receiving draft orders with ACH/wire payment.
• Cart Note Autofill for Wholesale
  Pre-fill cart note field with “ACH required” note for tagged users.
• (Shopify Plus Only) Use checkout.liquid or Functions
  Fully control available payment gateways at checkout using Shopify Plus features.

Shopify Embedded Solution (Best for Automation)

Custom Shopify Embedded App that enables you to automatically add payment transaction fees directly to customer payments.

Final Thoughts:

By utilizing all the solutions discussed, we can effectively overcome the challenges mentioned above in a B2B wholesale Shopify setup. Additionally, we have analyzed a few more common challenges that e-commerce managers and store owners often face. Stay connected with us for our next article, where we’ll dive into payment-related challenges. If you have any questions about implementation, feel free to connect with us!