E-commerce Payment Solutions with Shopify: What Are The Challenges, and What Can You Do?

A smooth payment process can make or break your online store. The simple truth is that around 70% of customers abandon their carts just because their preferred payment method isn’t available, or the checkout feels complicated. 

So, offering the right payment options is simply a must if you want to reduce checkout friction, capture more sales, and build trust with your shoppers.

While Shopify makes this easier with Shopify Payments, a built-in solution that handles transactions securely, it’s not always the perfect fit. Some regions don’t support it, and certain businesses need specialized payment providers for compliance, various industries, or international sales.

The good news is there are many e-commerce payment solutions that can help you accept payments efficiently, manage fees, and prevent issues like fraud or failed transactions.

In this guide, we’ll walk you through the main payment options on Shopify, the common challenges you might face, and practical strategies you can use to set up a reliable, optimized checkout.

What Are E-commerce Payment Solutions?

An e-commerce payment solution is any system that lets your online store accept money from customers. It’s essentially how someone goes from browsing your products to completing their purchase.

These solutions’ job is to make sure the transactions are secure, reduce the risk of fraud, and handle things like refunds, disputes, and compliance with financial regulations. 

Understanding E-commerce Shopify Payment Solutions

Shopify is one of the most popular platforms for running an online store because it simplifies many aspects of e-commerce, including payment processing. 

And while Shopify handles the basics for you, the platform also gives you flexibility to choose the right payment system for your business, ensuring you can make the best choice for your needs.

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Shopify Payments is Shopify’s native payment system. It’s designed to make transactions simple and reliable. Plus, since it’s fully integrated with your store, you don’t have to worry about connecting third-party solutions unless you want to.

Using Shopify Payments means you can:

• Accept major credit and debit cards directly
• Access built-in fraud detection tools
• Track payments and payouts right from your Shopify dashboard

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While Shopify Payments works well for most businesses, it isn’t always the only option. Here are some common reasons you might choose a third-party payment solution:

• Location restrictions: Shopify Payments isn’t available in every country, so you may need a local provider to accept payments in your region.
  
  
• Industry requirements: Industries with stricter regulatory requirements, such as adult products, gambling, or CBD, often require specialized solutions with higher risk tolerance.
  
  
• International sales: If you sell globally, you might need solutions that support multiple currencies or local payment methods for certain markets.
  
  
• Custom payment needs: Some businesses want options like Buy Now, Pay Later services or specific fraud protection tools not included in Shopify Payments.

The key is choosing the solution that balances convenience for your customers with compliance, security, and operational efficiency for your business.

Types of Payment Methods Supported by Shopify

Whether you’ve chosen Shopify Payments or a third-party provider, you can offer a variety of payment methods to match your customers’ preferences. The most common options include:

1. Credit and Debit Cards

• Accept Visa, MasterCard, American Express, and more
  
  
• Works through Shopify Payments or compatible third-party payment solutions

2. Digital Wallets

• PayPal, Apple Pay, Google Pay, and Shop Pay
  
  
• Speed up checkout and reduce friction

3. Buy Now, Pay Later Options

• Services like Klarna or Afterpay
  
  
• Helpful for higher-ticket items and boosting conversions

4. Recurring / Subscription Payments

• Supported by certain third-party solutions and apps
  
  
• Useful for stores offering subscription boxes, memberships, or recurring services
  
  
• Ensure your solution handles automated billing, customer notifications, and easy cancellations

5. Manual Payment Methods

• Bank transfers, cash on delivery, or money orders
  
  
• Useful for local customers or niche markets

6. Local Payment Methods

• Examples: iDEAL (Netherlands), Sofort (Germany), Bancontact (Belgium), POLi (Australia)
  
  
• Important for international customers who prefer local banking methods

7. Cryptocurrency Payments

• Some third-party solutions allow accepting Bitcoin, Ethereum, or other cryptocurrencies
  
  
• Useful if your business or audience is crypto-friendly

8. Prepaid Cards or Gift Cards

• Shopify supports selling and accepting gift cards as payment
  
  
• Can help with promotions and customer loyalty

9. Mobile Carrier Billing / SMS Payments (less common)

• Certain third-party apps allow charging purchases directly to a customer’s mobile bill
  
  
• Usually for digital goods or subscriptions

So while credit/debit cards, digital wallets, Buy Now Pay Later, and manual payments cover the majority of transactions, offering region-specific or alternative payment options can help capture international sales and niche audiences.

Common Challenges with E-commerce Payment Solutions on Shopify

Even with Shopify’s robust platform, accepting payments isn’t always straightforward. 

E-commerce store owners often run into challenges that can affect sales, customer trust, and overall business operations. Understanding these common issues is the first step toward solving them.

Technical Challenges

Integration Issues
Connecting third-party payment solutions or apps can sometimes be tricky. Compatibility problems with your Shopify theme, checkout apps, or custom scripts may cause errors during payment processing.

Payment Failures and Declines
Even when a customer enters the correct details, transactions can fail due to banking restrictions, fraud detection triggers, or technical glitches. Multiple failed attempts can frustrate customers and lead to abandoned carts.

Checkout Customization Limitations
While Shopify allows some customization, certain advanced features – like conditional payment methods or custom multi-step checkouts – may require additional apps or developer support.

Business Challenges

High Transaction Fees
Different solutions and payment methods come with varying fees. Shopify Payments has its own fee structure, and using third-party providers often adds extra transaction costs. For high-volume stores, these fees can quickly add up.

Chargebacks and Refunds
Managing refunds and disputes is time-consuming. Chargebacks not only cost money, but can also impact your standing with payment providers.

Multi-Currency and Cross-Border Payments
Selling internationally introduces extra complexity. Currency conversion fees, local banking rules, and customer expectations around preferred payment methods can create friction if not handled correctly.

Cart Abandonment
A complicated checkout process, limited payment options, or unexpected fees can lead to abandoned carts. According to research, checkout friction is one of the top reasons customers leave without completing a purchase.

Security and Compliance Issues

Fraud Prevention
Online payments are a target for fraud. Shopify provides built-in fraud detection, but industries with stricter regulatory requirements or international transactions may require extra tools and monitoring.

Regulatory Compliance
Businesses must follow local and international regulations around payments, data privacy, and PCI DSS compliance. Using the wrong payment method or solutions could expose your store to penalties or legal issues.

Stop Losing Customers at Checkout

Long, clunky checkouts cost sales. Through the FirmEU network, you can connect with trusted providers for fast, seamless payments, so customers can pay their preferred way.

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How To Overcome These Common Payment Challenges

Payment challenges are part of running an online store, but they’re far from roadblocks. With the right setup and a few smart adjustments, you can turn these obstacles into opportunities to boost conversions and strengthen customer trust.

1. Choose the right payment solution based on your region, industry, and target audience. Shopify Payments works for most stores, but industries with stricter regulatory requirements or international sales may need specialized providers.
   
   
2. Offer multiple payment options to reduce cart abandonment and give customers flexibility.
   
   
3. Use fraud prevention tools and monitor transactions regularly. Shopify has built-in protections, but third-party solutions can add an extra layer of security.
   
   
4. Streamline checkout by removing unnecessary fields and enabling fast payment methods like digital wallets.
   
   
5. Track fees and refunds in one dashboard to optimize costs and avoid surprises.

How to Choose the Right Shopify Payment Solution

The first step to solving payment challenges is finding the right solution for your store.

E-commerce businesses succeed when they choose payment systems that align with their store setup, customer preferences, and operational needs.

Here are our top recommendations for selecting a payment solution that works for your business:

1. Understand Your Business Needs

Before selecting a payment solution, think about your store’s requirements:

• Industry: Unlike low-risk businesses, industries with stricter regulatory requirements like CBD, adult products, or gaming often need gateways that can handle these types of businesses.
  
  
• Location: Shopify Payments isn’t available everywhere, so international businesses may need gateways that support multiple currencies or local payment methods.
  
  
• Customer preferences: Offering credit cards, digital wallets, or Buy Now, Pay Later options can directly impact conversions.

Need Better Payment Solutions?

Through the FirmEU network, you can connect with verified payment providers, so you can accept payments confidently and compliantly.

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For stores navigating multiple gateways, international sales, or industries with stricter regulatory requirements, a payment orchestration platform like PayFirmly can help streamline processes, route transactions efficiently, and reduce failed payments. 

Learn more about PayFirmly in our latest blog post!

2. Compare Shopify Payments and Third-Party Solutions

Some stores benefit from combining Shopify Payments with third-party solutions to maximize approval rates and provide more options for customers.

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For stores using multiple solutions, a payment orchestration service can help manage transactions, reduce failed payments, and simplify reporting.

3. Evaluate Key Selection Criteria

When choosing a payment solution, keep these factors in mind:

• Transaction fees and cost optimization: Compare costs across solutions and consider ways to reduce fees, such as combining Shopify Payments with third-party solutions or using payment orchestration.
  
  
• Supported payment methods: Make sure your customers can pay the way they prefer.
  
  
• Currency and country support: Essential if you sell internationally.
  
  
• Fraud detection and security features: Protect your business and your customers.
  
  
• Ease of integration: A simple setup saves time and reduces errors.

4. Test and Optimize Your Payment Setup

Once your payment solution is set up, it’s important to:

• Test checkout flows to ensure smooth transactions.
  
  
• Monitor declined payments and success rates.
  
  
• Adjust payment options based on customer behavior and preferences.

5. Why It Matters

The right payment solution keeps your store secure, reliable, and easy for customers to use. Choosing the right combination of payment options or using payment orchestration to simplify multiple solutions reduces failed transactions, streamlines your operations, and helps maximize your revenue.

A well-optimized payment setup does more than prevent problems. It builds trust with shoppers, improves conversion rates, and supports the growth of your business as you scale.

Best Practices for E-commerce Payment Success

Even with the right payment solution in place, following best practices ensures your Shopify store runs smoothly, and your customers have a seamless experience. Here’s what we recommend:

Offer Multiple Payment Options

Customers expect flexibility. Accept credit and debit cards, digital wallets, Buy Now Pay Later, and local payment methods if you sell internationally. The more options you provide, the fewer abandoned carts you’ll see.

Optimize Your Checkout Flow

A short, simple, and transparent checkout reduces friction. Remove unnecessary fields, show shipping and taxes upfront, and use express payment options like Shop Pay, Apple Pay, and Google Pay.

Make sure your checkout is mobile-friendly, with fast loading, easy-to-tap buttons, and forms optimized for smaller screens.

Prioritize Security and Compliance

Protect your business and customers with fraud prevention tools, SSL certificates, and PCI DSS-compliant payment solutions. Ensure your store meets local and international regulations to avoid penalties.

Monitor Performance and Transactions

Track payment success rates, declined transactions, and chargebacks. Analyze patterns to adjust payment methods or troubleshoot recurring issues before they affect revenue.

Leverage Payment Orchestration

If you use multiple payment solutions, consider payment orchestration solution like PayFirmly to streamline routing, reduce failed transactions, and simplify reporting. This is especially useful for international stores or high-volume operations.

Need a Payment Solution That Checks All The Boxes?

From fewer chargebacks, 500+ payment methods, and higher approval rates, PayFirmly solves the payment problems that are costing you customers.

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Test and Iterate Regularly

Regularly test your checkout flow, payment integrations, and customer experience. Small improvements can significantly boost conversions and customer satisfaction.

Keep Customers Informed

Display trust signals such as secure payment icons, clear refund and return policies, and order confirmations. Communicating clearly reduces hesitation and increases confidence.

Why PayFirmly Is The Ultimate E-commerce Payment Solution

At FirmEU, we’ve worked with countless Shopify businesses, and seen the same challenges we talked about on repeat.

These problems often leave store owners juggling multiple providers with little control. That’s where platforms like PayFirmly come in.

PayFirmly is designed to solve the gaps most e-commerce Shopify merchants face. It gives you smarter routing, stronger fraud prevention, and broader payment coverage, all in one flexible platform. 

Here’s how PayFirmly compares to traditional payment solutions:

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For e-commerce Shopify merchants, this means fewer failed transactions, lower costs, and happier customers at checkout. 

Through the FirmEU network, you can connect with providers like PayFirmly to find a solution that fits your e-commerce goals.

Start Accepting Payments Today

E-commerce payment challenges can slow your store, frustrate customers, and cost sales, but they don’t have to. 

By choosing the right Shopify e-commerce payment solutions, offering multiple options, and optimizing your checkout, you can overcome these obstacles and make payments simple, secure, and reliable.

Through FirmEU’s network, businesses of all industries can connect with trusted payment providers that fit their specific needs.

From finding the right solutions to managing multiple providers across regions, FirmEU connects you to the partners that make it possible to accept payments confidently, reduce failed transactions, and scale globally.

Take control of your checkout experience and start turning payment challenges into opportunities today!

E-commerce Payments Made Easy

Through the FirmEU network, you can connect with verified payment providers that make it simple to accept payments from anywhere your business grows.

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