What if the way you process payments is quietly eating away at your profit margins? For business owners, the choice between different payment gateways should be driven by more than convenience. The payment system for your business can make or break long-term growth. So, let’s compare two common eCommerce gateways: Authorize.net vs Shopify Payments. Knowing which platform best fits your model is essential.
Overview of Authorize.net vs Shopify Payments
Authorize.net
Owned by Visa, Authorize.net is one of the oldest and most trusted payment gateways on the market. It’s a reliable choice for businesses that want flexibility in how they accept credit card transactions. This platform is particularly attractive to established businesses with custom setups. It works with a variety of POS systems, ecommerce solutions, and partnered payment providers like ECS Payments.
Shopify Payments
Shopify Payments is an integrated solution designed specifically for Shopify merchants and is powered by Stripe. For anyone running a Shopify store, this is the most seamless way to handle accepting payments. It eliminates the need for third-party processors and centralizes your transactions within the Shopify admin dashboard.
Authorize.net vs Shopify Payments Feature Comparison
Supported Payment Methods
Authorize.net supports credit card payments, eChecks, and a variety of third‑party payment methods. Shopify Payments focuses primarily on card transactions and digital wallets like Apple Pay and Google Pay.
Recurring Billing and Subscriptions
Authorize.net shines for businesses managing subscriptions or installment plans. It offers tools like Automated recurring billing and a Customer Information Manager for securely storing customer payment data. Shopify Payments offers subscription tools through third‑party apps, which can add to the overall cost.
Fraud Detection and Security Tools
Authorize.net includes an Advanced Fraud Detection Suite, along with analytics and reporting to help you monitor suspicious activity and reduce chargebacks. Shopify Payments provides basic fraud protection, though third‑party add‑ons may be required for more advanced needs.
Ease of Integration
Authorize.net works with a wide range of eCommerce platforms and POS providers, making it a strong choice for businesses with complex or multi‑channel setups. Shopify Payments is designed for Shopify stores only, which limits flexibility but simplifies operations for merchants fully invested in that ecosystem.
Merchant Dashboard And Reporting
Authorize.net gives access to a detailed dashboard with tools that help merchants track transactions, manage recurring billing, and monitor their account activity. While it’s powerful, some business owners may find the interface a bit dated. Shopify Payments, on the other hand, integrates directly with the Shopify admin panel, making it easy to view sales performance, track cash flow, and manage day‑to‑day operations in one place.
Customer Support Responsiveness
Authorize.net provides around‑the‑clock live support, which is a major plus for businesses that can’t afford downtime. This is especially reassuring if you run into an issue outside regular business hours. That said, the speed and depth of help can depend on the complexity of your problem. Shopify Payments leans on Shopify’s broader support network, which gives merchants access to a large team, quick chat responses, and a deep library of how‑to guides and troubleshooting resources.
Developer Tools and API Availability
If you need room to build out custom workflows or connect with other systems, Authorize.net gives you plenty of options. Its API tools are designed for developers who want to go beyond the basics and really tailor how payments fit into their operations. Shopify Payments also has API access, but it’s locked into the Shopify ecosystem. That works fine if you plan to stay fully within their platform, but it leaves little flexibility if your business needs to connect with outside tools or more complex setups.
Authorize.net vs Shopify Payments Fees and Pricing
Authorize.net offers two pricing options:
- All‑in‑One: $25 per month plus 2.9% + 30¢ per transaction. This includes a merchant account, payment gateway, fraud detection, recurring billing, and 24/7 live support.
- Gateway‑Only: $25 per month plus 10¢ per transaction and a 10¢ daily batch fee, designed for businesses that already have a merchant account but want to use Authorize.net as their payment gateway.
Shopify Payments, by contrast, has no monthly gateway fee beyond the cost of your Shopify plan. Shopify Payments uses a tiered model based on your subscription plan. For online transactions, processing fees start at 2.9% + 30¢ on the Basic plan, 2.7% + 30¢ on the Grow plan, and 2.5% + 30¢ on the Advanced plan. In‑person rates are slightly lower, ranging from 2.6% + 10¢ down to 2.4% + 10¢, depending on the plan.
If you use a third‑party payment provider instead of Shopify Payments, Shopify adds an extra fee of 2% on the Basic plan, 1% on the Grow plan, and 0.6% on the Advanced plan. For Shopify Plus stores using Shopify Payments as their primary gateway, these additional fees are waived, including on transactions involving store credit or gift cards.
As of May 12, 2025, Shopify also applies third‑party transaction fees when orders include store credit or gift cards for new stores.
Utilizing ECS Payments For A Smarter Way to Process
This is where ECS Payments can make a real difference. As a merchant services provider, ECS can work with Authorize.net or Shopify Payments to help you reduce processing costs, optimize your pricing structure, and avoid unnecessary fees.
Whether you need a full‑service all‑in‑one setup with Authorize.net or want to streamline costs while staying on Shopify, ECS provides custom solutions that improve cash flow and support growth.
Beyond pricing, ECS delivers personalized onboarding, advanced fraud support, and access to POS solutions like Clover and Dejavoo, giving your business tools that go beyond what you’d get by signing up directly with either platform.
Chargeback Policies
Both platforms charge fees for chargebacks. Chargebacks are a significant risk area for merchants, making strong fraud prevention a critical factor in deciding on a processor. When chargeback rates exceed roughly 1 % of sales, merchants face higher scrutiny and fees from banks. That makes effective fraud tools a critical consideration.
In 2024, nearly three out of four merchants reported an increase in friendly fraud chargebacks. By 2025, every dollar lost to fraud is projected to cost U.S. merchants about $4.61, reflecting a 37% increase compared to 2020. If this trend continues, merchants could be facing approximately $28.1 billion in annual losses from chargeback fraud by 2026, which would represent a 40% increase from 2023.
Pros and Cons
Authorize.net
- Pros: Broad compatibility, advanced fraud protection, strong support for recurring payments, and offers high-risk flexibility for businesses.
- Cons: Higher setup complexity and ongoing monthly fees.
Shopify Payments
- Pros: Seamless integration with Shopify Store, no separate gateway required, transparent pricing tiers.
- Cons: Exclusivity to Shopify stores, limited flexibility for third-party integrations, and does not accommodate high-risk businesses.
Ideal Use Cases
Who Should Use Authorize.Net?
Businesses that operate both online and in-store, or those needing advanced fraud controls and recurring billing, will find Authorize.net a strong fit.
Who Should Choose Shopify Payments?
If your business runs entirely on Shopify and you want to keep everything in one place, Shopify Payments makes that easy. It removes the need to manage multiple accounts or juggle separate providers, which can save time and reduce the chances of errors. For store owners who value convenience over customization, this built‑in option keeps payment processing simple and fast.
ECS Payments: A Trusted Alternative
Deciding on the right gateway for your business, Authorize.net vs Shopify Payments, really comes down to what matters most for your specific needs. If you need a flexible system that can adapt to complex setups, Authorize.net is worth considering. If your priority is speed and simplicity within the Shopify ecosystem, Shopify Payments delivers that.
For merchants who want more control over their costs and flexibility in how they accept payments from customers, ECS Payments offers a strong alternative. Whether you’re interested in integrating advanced POS terminals from Clover or Dejavoo, or you need a custom setup to bring your processing fees down, ECS can build solutions tailored to your business. Our team works directly with merchants to simplify onboarding, reduce transaction costs, and ensure you’re getting the most out of your payment systems.
If you’re ready to explore better payment solutions, ECS Payments can walk you through your options and help you implement a strategy that supports your growth.
