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Flagship Merchant Services vs Square: Which Wins Out in 2024?

Ashley Hague Ashley HagueFinance Specialist
As I’m sure you’ve discovered in your search for the perfect credit card processor, there are so many different options. Flagship Merchant Services and Square Payments are two prominent players in the payment processing industry that are often touted as great processors for small businesses. But which one is better?

Both options have their unique strengths, but I dove deep into each processor’s features, pricing, support, and more to help you determine which one best suits your business.

Square offers simple pricing, no monthly fees, and a ton of versatile features aimed at newer startups or smaller businesses. Flagship, on the other hand, is an excellent choice for businesses that are more established or have ambitions to scale. With its personalized approach and dedicated account managers assigned to each customer, Flagship excels at providing tailored solutions and guidance.

Overall, I think Flagship is the best bet for affordability, ease of use, and personalized support. You can request a free quote from Flagship, or read on to see why Flagship is my overall winner.


Square’s Built-In Features Are Ideal for Business Owners Across Industries

Square's POS options
Square’s range of POS options are perfect for startups
When it comes to point-of-sale (POS) solutions, both Flagship and Square offer impressive features.

Square’s POS system immediately caught my attention with its renowned user-friendly interface. Square provides a range of hardware options, including mobile card readers, terminals, and cash registers, all seamlessly integrated with its software. However, only the magstripe reader is free with a basic account, while the other options start at $149.

Flagship offers a free terminal1 (when you sign up for a contract) or you can buy the equipment outright. It offers customized solutions tailored to your specific business needs using Clover or Verifone systems, which are highly regarded in the industry as reliable and secure choices.

Both processors offer specific solutions for restaurants, retail, and mobile businesses. Though the offerings are similar, Square is better for newer businesses that have lower sales volume, while the POS systems offered by Flagship can more readily handle higher sales volumes across locations.

Additionally, Flagship and Square have comprehensive e-commerce offerings. Square’s suite of tools, including its website builder and customizable online store templates1, allow you to establish a strong online presence through its all-in-one platform. This is great for building a free basic site without dealing with complicated APIs or incompatible software. However, it’s quite limited in its functionality and won’t provide the same benefits as a custom-made website.

In contrast, Flagship provides shopping cart integrations and a secure payment gateway through its Authorize.Net partnership. These allow you to integrate the payment system with your existing website or e-commerce platform. While more customizable, it’s not as simple or easy to use as Square’s built-in tools.

Pirq Digital Loyalty overview
Flagship partners with Piqr to enable you to set up a loyalty system for your business
Square also boasts an array of proprietary features like recurring billing, invoicing, appointment setting, and loyalty programs. While some of these features are also available with Flagship – like a digital loyalty program through Pirq – they aren’t as robust or easy to use as Square’s ecosystem.

These payment processors offer a number of features and hardware options that are ideal for small businesses. Ultimately, Square’s features are slightly more impressive, with several free options to help your business thrive.

Ease of Use

Square Is Simple To Use, While Flagship Offers a Dedicated Account Manager

Both Flagship and Square offer streamlined processes for quick and easy sign up. Square’s online application requires minimal documentation and it only takes a few minutes to complete1. Once approved, Square allows you to start processing payments almost instantly. However, because of its simplicity, there are a number of complaints online about unexpected account terminations due to missing key information in the signup process.

Flagship’s application also begins online but does require a call with a sales representative to complete. This is a bit more cumbersome than an online process, but it also ensures that you’ll submit all the required information to receive a personalized quote to meet your unique business needs. You’ll also avoid costly account freezes that are common with Square.

iAccess Reporting Dashboard overview
Flagship’s iAccess reporting dashboard gives you an overview of your whole business
For setup assistance, Square offers self-setup options, online guides, and customer support. Flagship goes the extra mile with a dedicated account manager who not only assists you during the application but also with setup and integration, ensuring a smooth transition.

One area where Flagship truly impressed me is its reporting tool, iAccess. While Square offers basic reporting capabilities, Flagship’s robust reporting and analytics tools1 can provide your business with free comprehensive insights including detailed sales reports, customer behavior analysis, and comparisons against other businesses. It’s simple and intuitive, for easy tracking.

You won’t go wrong with either of these options when it comes to ease of use. However, because of the dedicated account manager, high approval rate, and more advanced reporting features, I think Flagship manages to secure the win for this category.

Compliance and Security

Both Offer Industry Standards, but Square Goes the Extra Mile

Security is one of the biggest factors I considered when comparing these two payment processors. While Flagship and Square offer enhanced fraud detection capabilities to protect your business, they differ in the exact types of compliance offered.

Flagship’s POS and e-commerce tools offer industry-leading security including encryption, tokenization, and address verification (AVS). These go a long way to prevent and catch fraud before it affects your business. It’s also GDPR and CCPA compliant to cover any European or Californian privacy requirements.

However, you’ll need to pay $99/year to maintain PCI compliance through the self-assessment questionnaire with Flagship. This is on par with many other credit card processors, but it’s a hefty sum compared to Square, which doesn’t charge any PCI compliance costs. In fact, with Square, you don’t have to worry about PCI at all.

Square's industry-leading security features
Square’s advanced security features are some of the best in the industry
As a payment aggregator, Square assumes the responsibility of PCI compliance1, so you don’t have to maintain and validate your own compliance. Square stands out by also offering built-in HIPAA compliance for businesses dealing with sensitive healthcare data. In addition to these compliance features, Square implements end-to-end encryption and tokenization to protect payment data.

Considering the ease and convenience provided by Square in terms of PCI compliance, along with its additional security measures, I believe Square offers the best overall security solution. With Square, you can focus on your business while relying on its robust security infrastructure.

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Flagship Is Less Transparent, but Offers Better Rates

Flagship offers a personalized approach and tailors rates according to your specific business needs. It claims to have some of the lowest rates in the industry and Flagship even offers a $200 meet-or-beat guarantee1. This means Flagship will work with you to find a suitable rate for your business.

Although I must admit that it’s frustrating that Flagship’s pricing isn’t available on its website, the ability to negotiate and potentially secure more favorable rates is a definite advantage. When it comes to overall cost, Flagship’s personalized rates often make it a more cost-effective choice for high-volume businesses.

On the other hand, Square takes a different approach with its transparent and straightforward pricing. As a small business or startup, you may appreciate Square’s interchange-plus pricing model. There are no long-term contracts to worry about, and Square even offers a basic plan with no monthly fees. This is particularly good if you don’t need the extra features. However, if you want any add-ons, the monthly fees will generally be higher than Flagship.

It’s important to consider your business size, sales volume, and your specific needs when making a decision. Based on my assessment, Flagship stands out as the top recommendation, thanks to its comprehensive features, personalized approach, and more affordable pricing.

To see the pricing models side-by-side, check out the table below.
Flagship Merchant Services Square
Monthly fee on the cheapest plan $7.95 $89.00
Transaction fees on the cheapest plan 1.58% + 19¢ (in person) 2.5% + 10¢
POS equipment
  • Clover Mini
  • Clover Station
  • Clover Flex
  • Clover Go
  • Verifone Terminal
  • Magstripe reader
  • Square Terminal
  • Square Stand
  • Square Register
E-commerce features Website builder, virtual terminal, third-party integrations Shopping cart integrations and virtual terminal through Authorize.Net
Payout times 48 hours, with same-day funding available (extra fee) 48 hours, with same-day funding available (extra fee)
PCI assistance $99/year Not required
Fraud detection tools
Customer support 24/7 technical phone support Telephone, email, chat, online knowledge base


Flagship’s 24/7 Support Comes Standard, While You’ll Have to Pay With Square

Both payment processors strive to provide timely and professional assistance – but only one really succeeded.

Flagship’s dedicated account managers ensure a reliable response time and a high level of professionalism in its interactions. There is also a basic FAQ section on the site, which I found helpful but not overly robust. Luckily, it’s easy to get help when you need it, as Flagship offers 24/7 technical phone support, which is available for all customers.

Square, on the other hand, offers customer support through various channels such as email, phone, and a comprehensive online help center. However, it’s important to note that its 24/7 support is only available to premium customers. This means that businesses on lower-tier plans will have limited access to round-the-clock assistance.

email confirmation from Flagship
I received an automated email to confirm my contact page submission
I reached out to both companies to gauge how well they respond. With Flagship, I sent a message through the online contact page and received confirmation that my message went through almost immediately. Then I received a call from the sales team the next day. Though I missed the actual call, I appreciated how quickly the team reached out.

email response I received from Square
Square’s response to my email as an account holder was fast and simple
I sent Square support a message through the online contact page as well, pretending to be a prospective customer. Days later, and I still haven’t received a response or even confirmation that my message went through. While frustrating, I also reached out by email several weeks after signing up to an account and found that response quick and helpful. So it seems like Square prioritizes existing account holders over prospective customers.

Despite the comprehensive online help center that Square offers, I think that Flagship’s quick response and standard 24/7 support are better overall.

Flagship’s Personalized Approach Works Best for Most Small Businesses

After diving deep into the features and offerings of Flagship and Square, I believe that Flagship is the better overall credit card processor. With its personalized support, dedicated account managers, and tailored solutions, Flagship truly understands what it takes to make your business shine.

Square is easy to set up and good for startups or businesses with simpler payment processing needs, but may cost you more in the long run. Flagship is more customizable, and while less transparent upfront, will generally offer more affordable pricing and more features that can help your business grow. By opting for Flagship, you’ll have the expertise and resources you need to optimize your payment processing operations and drive your business growth.

Here’s a final comparison for you.

Flagship Merchant Services
Several POS systems to choose from and advanced merchant solutions like online payment and shopping cart integrations, and gift card and loyalty programs
Proprietary POS systems to suit specific businesses and an all-in-one platform with a simple e-commerce website builder
Ease of Use
Dedicated account manager for custom support and smooth onboarding and iAccess advanced reporting and analytics
Online application process, quick onboarding, and basic reporting functions
PCI, GDPR, and CCPA compliant
PCI DSS Level 1 with in-house fraud detection, ISO 270001, and HIPAA compliant
Low monthly fees with either tiered or interchange-plus pricing options
Basic plan with no monthly or chargeback fees, but additional features for a cost
24/7 technical phone support and email support
Online knowledge base and email, phone, and chat support during business hours


What types of businesses are best suited for Flagship?

Flagship Merchant Services is an ideal choice for businesses of various sizes and industries, including retail, restaurants, online, and service-based operations. Flagship caters to those seeking a tailored approach, whether they are established enterprises or small businesses looking for guidance throughout the payment processing journey.

Are there any setup fees or monthly charges associated with using either Flagship or Square?

Flagship typically does not charge setup fees, but it may charge monthly fees depending on the specific services and solutions you choose. On the other hand, Square does not have any setup fees with no monthly charges for its basic payment processing services. However, additional features or advanced solutions such as loyalty programs or accounting software may have associated monthly costs.

Can I use existing POS software with either Flagship or Square?

Flagship provides support for integrating existing POS systems with its own, allowing you to continue using your preferred software without purchasing new devices. Square, on the other hand, only offers its proprietary software options for customers to use. That means you won’t be able to take your Square POS system elsewhere if you decide to leave.

Which is better for e-commerce, Flagship or Square?

For e-commerce, Square is generally considered a better option. Square offers a comprehensive suite of e-commerce solutions, including a website builder, integrations with popular e-commerce platforms like Shopify, and features like inventory management and order fulfillment. For more popular e-commerce options, check out our top ten credit card processors in 2024.

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