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6 Best E-Commerce Merchant Services in 2024

Kamso Oguejiofor Kamso OguejioforFinance Specialist June 17, 2024
June 17, 2024
You’re probably searching for the perfect merchant account and staring at endless options, worried about hidden fees, complex integrations, expensive rates, and whether your choice will scale as your business grows. That’s perfectly normal. You don’t want to end up with a service provider that gives you more problems than solutions.

Ideally, the best way to process online payments is to use a top-tier, low-cost credit card processor that lets you access a well-known payment gateway. This is much cheaper than options like PayPal or Venmo, and in most cases, it’s cheaper than using the gateway (e.g., Authorize.net) directly.

What’s more, a reputable payment processor will help you maintain PCI compliance so you don’t have to worry about fines. You’ll also get features like chargeback protection, free POS equipment for when your e-commerce store expands, reports and analytics tools, and much more.

So, as your friendly neighborhood researcher, I took a deep dive into 50+ merchant service providers, carefully evaluating their e-commerce features, ease of use, pricing, and support. Leaders Merchant Services came out on top because of its industry-low fees and extra features, like a shopping cart integration. That said, read on to explore all of my recommendations and see which resonates best with your business needs.

Short on Time? These Are the Best E-commerce Merchant Services in 2024

  1. Leaders Merchant Services1 – Negotiable, industry-low rates for e-commerce businesses.
  2. Square1 – Transparent pricing with free features for new online businesses.
  3. Flagship Merchant Services1 – Straightforward application process and a digital loyalty program.

See 3 More Great Options | Comparison Table

What We Look For in the Best E-Commerce Merchant Services

  • Payment gateway offering. Payment gateways are an important part of online commerce, as they are responsible for collecting and encrypting your customer’s payment information. All my recommendations either have a built-in payment gateway or integrate with a trusted third-party gateway.
  • Affordable transaction fees. High transaction costs can eat into your profits, so I ensured I included cost-effective merchant services with transparent pricing.
  • Seamless integrations. I only included options that integrate smoothly with your e-commerce platforms, shopping carts, accounting software, and other tools so you can avoid operational disruptions.
  • Support for multiple payment methods. E-commerce businesses generally cater to a diverse customer base, so I made sure my recommendations accept various payment options, including credit/debit cards and digital wallets.

Leaders Merchant Services (LMS) offers some of the lowest processing fees in the industry, starting from ~0.15% + $0. Not only that, but it also allows you to negotiate a price that’s more suitable for your business needs. LMS even wagers a $200 gift card that it can match your current rates or offer better rates.

I’m a big fan of LMS’s shopping cart tool, CartManager. Integrating this secure shopping cart into your online store will allow you to automatically add “add to cart” buttons to your website, retrieve customer statistics for business analysis, and calculate tax and shipping costs. You’ll even be able to display your cart in multiple languages to cater to international customers.

One of the benefits of being an LMS merchant is that you can get a cash advance. This especially benefits up-and-coming e-commerce businesses seeking additional capital to fuel their growth. The best part is that there is no payback deadline or required collateral – you simply pay back through small commissions on future transactions with LMS.

Features and Benefits

  • High approval rate. LMS has a 98% approval rate. So, even if your products fall within a high-risk industry or if your e-commerce business has a poor financial history, there’s a high chance LMS would give you a chance.
  • Authorize.net payment gateway. LMS integrates with Authorize.net, a widely used payment gateway and virtual terminal. Authorize.net comes with end-to-end encryption to ensure that all your transactions will be kept secure.
  • Dedicated chargeback department. As an LMS merchant, you can access a 24/7 chargeback department to assist you with chargebacks or fraud-related situations.
  • Free POS equipment. If you sign a long-term contract with LMS, you’ll get free POS equipment. This is a great way to minimize costs if you have a physical store that complements your online business.
For more details, check out our comprehensive LMS review.

Software integrations Authorize.net,
CartManager, Quickbooks
Payment methods
accepted
Credit and debit cards,
digital wallets, ACH,
bank transfers
Security features PCI-compliant, advanced
fraud detection and
prevention, end-to-end
encryption, tokenization
Transaction fees on
cheapest plan
~0.15% + $0
Monthly fee on cheapest
plan
$9.00

2. Square: Best for New Online Businesses1

Square lets you create an online store for free (you can also connect to an existing store). Online store features include showing personalized recommendations to returning customers, highlighting new products and top sellers to move specific inventory, and scheduling product drops, flash sales, and discounts to launch automatically.

Signing up for Square is super easy. You can create an account and start accepting payments on the same day. Provide some basic, necessary information, and you’re good to go. However, make sure you complete your profile thoroughly to avoid any unexpected account suspensions or terminations.

Square is one of the few merchant services that offer a plan without monthly fees. With it, you only have to pay a per-transaction fee of 2.6% + 10¢. Alternatively, some plans have monthly fees but better features, like the Square Plus plan at $89.00/month. It includes everything in the free plan plus extras like a free domain for 1 year, QR code ordering, customer accounts, and much more.

Features and Benefits

  • Software integrations. Square seamlessly integrates with popular e-commerce platforms like Shopify, WooCommerce, WordPress, Wix, and Ecwid. It also integrates with other business software like ZohoBooks, QuickBooks, and ActiveCampaign.
  • Advanced business software. Square offers free business tools like dashboard and reporting tools, scheduling and time-tracking software, in addition to the third-party integrations above.
  • FDIC-insured business checking account. With Square’s small business checking out, you can access your sales proceeds instantly. Signing up for this account is straightforward – you don’t need to go through any paperwork or credit check, and there are no monthly fees.
  • Sell without a website. You can sell your products online using Square’s buy buttons/QR codes. You don’t need a website for this – just create these links and share them with your customers through social media or email.
Read our full Square review for more details.

Software integrations Shopify, WooCommerce,
WordPress,
ActiveCampaign
Payment methods
accepted
Credit and debit cards,
digital wallets, ACH, bank
transfers
Security features PCI-compliant, end-to-end
encryption, tokenization,
two-factor authentication,
handles PCI compliance
for you
Transaction fees on
cheapest plan
2.5% + 10¢
Monthly fee on cheapest
plan
$89.00
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3. Flagship Merchant Services: Straightforward Application Process1

Flagship Merchant Services’s onboarding process is so fast that you can get your account approved in a couple of hours. There are no set-up fees, and you don’t need to provide all the usual documents. You just need to fill out some basic details, and a representative will contact you to complete the application process.

One of my favorite Flagship offerings is its custom gift card program. Gift cards are a great way to increase your revenue and customer base. You can also use Flagship’s gift cards instead of cash for merchandise returns. So whenever a customer returns a product, you can refund them with a gift card rather than cash.

Flagship provides month-to-month contracts without early termination fees. Plans start from as low as 1.98% + 0.21¢ (online) per transaction and $7.95/month. However, if you sign up for a long-term contract, you’ll get a free terminal, which is great if you have a physical storefront. Just note the device does come with a small insurance and maintenance fee.

Features and Benefits

  • Merchant cash advance. Flagship provides merchant cash advances for small and mid-sized businesses. The funding process is quick and easy, and you can get up to $150,000 if approved. You then repay the funds through a percentage of your daily debit and credit card transactions.
  • Digital loyalty program. Flagship partners with Pirq, a loyalty program, to enable you to track your customers’ buying trends and reward them accordingly. It’s a great way to drive repeat purchases.
  • iAccess business management portal. This portal helps you track your store’s sales volume, generate statements, and analyze competitors to make informed decisions for your e-commerce business.
  • MobilePay by PaySafe. MobilePay by PaySafe is Flagship’s free mobile app. It allows you to accept keyed-in payments through your phone, allowing you to process payments anywhere in the world.
Our expert Flagship review has more info on rates.

Software integrations Authorize.net, Flagship API
supports multiple
integrations
Payment methods
accepted
Credit and debit cards,
digital wallets, ACH, bank
transfers
Security features PCI-compliant, end-to-end
encryption, tokenization,
advanced fraud detection
and prevention, payer
verification
Transaction fees on
cheapest plan
1.98% + 0.21¢ (online)
Monthly fee on cheapest
plan
$7.95

Stax integrates seamlessly with e-commerce platforms like Shopify, WooCommerce, and Adobe Commerce (Magento). It also provides a pre-built shopping cart you can quickly add to your website. Alternatively, you can build a custom shopping cart using the Stax API. If someone on your team has technical skills, or if you can hire someone, it’s an excellent option for solid branding.

If your e-commerce store gets many repeat customers or sells subscriptions, you’ll appreciate Stax Bill, a tool that automates your billing processes. With Stax Bill, you can reduce customer churn and revenue leakage, increase payment accuracy and consistency, and maximize your business’ subscription growth.

I like how simplified Stax’s payment model is. Its subscription-style pricing includes a low, flat transaction rate of 0% + 10¢ (online) with zero markup on interchange fees. That said, the monthly fee starts from $99.00, so I’d recommend Stax for businesses earning at least $8,000 monthly. If that’s you, Stax’s model can save you up to 40% on payment processing fees.

Features and Benefits

  • Zapier integration. In addition to the direct integrations that Stax provides, such as with Shopify, it gives you access to hundreds of other third-party software tools via Zapier.
  • Stax Pay. This is Stax’s all-in-one payment platform for exploring sales data, viewing customer information, creating invoices, and scheduling payments.
  • Multiple payment gateways. Stax provides access to both Authorize.net and NMI payment gateways. This gives you more choice than most other merchant services.
  • Stax Connect. If you run a SaaS business, you can use Stax Connect to integrate payments on your software platform and provide a smooth payment process for your merchants.
Our full Stax review has more details.

Software integrations Shopify, WooCommerce,
Zapier, Authorize.net
Payment methods
accepted
Credit and debit cards,
digital wallets, ACH, bank
transfers
Security features Level 1 PCI-compliant,
tokenization, end-to-end
encryption, multi-factor
authentication, advanced
fraud detection and
prevention, payer
verification
Transaction fees on
cheapest plan
0% + 10¢ (online)
Monthly fee on cheapest
plan
$99.00

5. Payment Depot: Low Transaction Fees With Good Shopping Cart Support1

Payment Depot is a subsidiary of Stax, so they offer similar deals and features. For instance, like Stax, Payment Depot offers pre-built shopping cart templates that you can install and start selling with immediately. But if you prefer to create your custom shopping cart, there’s an option for that as well.

To help you avoid fraudulent transactions, Payment Depot has a 24/7 risk monitoring team that constantly monitors new fraud tactics and changes in bank policy. The team takes a proactive approach, preventing problems before they occur. You can also dispute any issues directly from your Payment Depot account, which will save you a lot of time.

Like Stax, Payment Depot offers a simplified, flat-rate pricing plan with a per-transaction fee of 0% + 10¢ (online) and a minimum monthly fee of $79.00. However, it also has an interchange-plus plan with zero monthly fees that starts from 0.2%-1.95% and is suitable for small to medium-sized e-commerce businesses. My only major complaint is that Payment Depot’s live chat and email communication is rather slow.

Features and Benefits

  • Comprehensive payment dashboard. You can manage many of your business operations within your Payment Depot dashboard. These include tracking sales performance, manually keying in card details, creating and sending payment links and branded invoices, and running promotions.
  • Free Dejavoo terminal. Every Payment Depot merchant is entitled to a free Dejavoo terminal, allowing you to save on hardware costs. (You can also pay for a different device if you choose.)
  • Next-day payouts. Payment Depot offers next-day deposits as standard, so you can expect to receive your funds in your bank account within 24 hours after processing them.
  • Great phone support. Payment Depot’s phone support makes up for its poor live chat and email support. When you call them, you’ll always reach friendly representatives who are willing to engage with you and help you solve any issues.
Check out our full review to learn more about Payment Depot.

Software integrations Shopify, WooCommerce,
Magento, BigCommerce,
QuickBooks, Authorize.net
Payment methods
accepted
Credit and debit cards,
digital wallets, ACH,
bank transfers
Security features Level 1 PCI-compliant,
tokenization, end-to-end
encryption, payer
authentication, 24/7 fraud
risk monitoring
Transaction fees on
cheapest plan
0% + 10¢ (in-person)
Monthly fee on cheapest
plan
$79.00

6. Chase Payment Solutions: Simple Pricing Plus an Integrated Bank Account1

Chase Payment Solutions offers next-day funding as standard, but you can get same-day payouts by signing up for a Chase Business Banking account. The business checking account has other features, like taking payments with your iPhone. The bank account costs $15/month, but you can waive the fee if you maintain a $2,000 minimum daily balance.

Chase also has a direct partnership with BigCommerce, so the integration process between your BigCommerce store and Chase Payment Solutions is straightforward. All you need to do is contact your Chase account manager, and they’ll assist you with the linking process.

Online transactions with Chase cost 2.9% + 25¢ per transaction. It’s a bit more costly than my other merchant services listed above. However, considering that there are no monthly fees and the perks you get if you opt into the checking account, I’d say it’s not a bad investment at all.

Features and Benefits

  • Customer Insights. Customer Insights is Chase’s powerful business analytics software. It makes it easy to monitor your sales, compare sales trends against competitors, view customer demographics, and track the time of day your customers mostly shop.
  • Gateway and virtual terminal. Chase integrates with Authorize.net (a payment gateway and virtual terminal) and the Orbital virtual terminal. Both are excellent options for receiving card-not-present transactions.
  • Multiple specialized payment software. Chase powers or integrates with 10 specialized business software tools, like FuseBill for managing subscriptions, BuilderTrend for project management and invoicing, and many more.
  • Comprehensive developer toolkit. If Chase doesn’t provide the specific software solution you need, you can develop it yourself. The developer toolkit includes documentation to guide you through the integration process and a sandbox environment for testing your development.
To learn more, check out our comprehensive Chase review.

Software integrations BigCommerce,
Authorize.net, Orbital
Payment methods
accepted
Credit and debit cards,
digital wallets, ACH, bank
transfers
Security features PCI-compliant,
tokenization, end-to-end
encryption, advanced fraud
detection and prevention,
payer verification
Transaction fees on
cheapest plan
2.9% + 25¢
Monthly fee on cheapest
plan
N/A

Go With One of These E-commerce Merchant Services

If you want to process online payments, you will need a cost-effective merchant service that provides a payment gateway, whether proprietary or third-party. Fortunately, my recommendations fall under this category.

If you’re looking for the most affordable fees, I recommend Leaders Merchant Services1. It provides extremely low rates but also allows you to negotiate better rates when you contact the support team. It also provides a secure shopping cart tool to easily integrate into your e-commerce store.

If you’re just starting your e-commerce journey, consider Square instead. Square is great for new online businesses1 because it offers many free good-to-haves, such as a ‘free’ plan with an online store builder.

Lastly, if you want to start accepting payments the same day you apply for a merchant account, open an account with Flagship Merchant Services1 – you can start selling in a couple of hours. The gift card and loyalty programs are also great to have.

If you’re still on the fence, here’s a quick breakdown of the best merchant services for online businesses.
Best Feature Best For Monthly fee
on cheapest
plan
Transaction
fees on
cheapest plan
Leaders
Merchant
Services
Low, negotiable fees and shopping cart tool E-commerce businesses that want to negotiate the best possible rates $9.00 ~0.15% + $0
Square Free online store builder New e-commerce businesses looking to minimize costs $89.00 2.5% + 10¢
Flagship
Merchant
Services
Fast onboarding process Businesses looking to accept payments as soon as possible $7.95 1.98% + 0.21¢ (online)
Stax
Payments
Simple pricing plans with low transaction fees Online businesses earning at least $8,000 a month $99.00 0% + 10¢ (online)
Payment
Depot
Flat-rate pricing and low interchange rates SMBs looking for simple pricing $79.00 0% + 10¢ (online)
Chase
Payment
Solutions
Fast payouts and business checking account Online merchants also looking for a business bank account N/A 2.9% + 25¢

FAQ

Who is the best merchant service provider?

The best merchant service provider is Leaders Merchant Services. It provides extremely low processing fees and gives you the opportunity to negotiate for even lower rates. It also provides a shopping cart tool for e-commerce stores and access to the trusted Authorize.net payment gateway. Plus, there’s a cash advance program for new businesses.

What are e-commerce merchant services?

E-commerce merchant services allow you to accept online payments from your customers. These typically include a credit card processor and a payment gateway, which securely transmits online payment information to the bank for authorization.

What is the best payment gateway for ecommerce?

Generally, Authorize.net. It’s widely trusted, and great payment processors, such as Leaders Merchant Services, often offer access at a reduced cost. However, there are other options out there, like NMI. You can check out our list of the best payment gateways for e-commerce to learn more.

What is an example of an e-commerce merchant?

An e-commerce merchant is any business that sells products or services online. The term refers to large companies like Amazon or Etsy and smaller businesses that sell through their websites or online marketplaces. The most common way to accept online payments is through a reputable credit card processor. See our list of the best credit card processors to learn more.

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