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Flagship Merchant

Services Review

Overall Rating

4.1/ 5.0

In-Depth Analysis



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Businesses of various sizes should seek out merchant account providers to partner with based on several factors, how long the company has been in business, what kind of third-party vendors it partners with to resell their products or services, along with how a company manages the front-end client support needs and the seamless back-end logistics of such partnerships. Flagship Merchants Services crushes those criteria as it has put in the years – it has been operating since 2001 from Charlestown, Massachusetts. It partners with one of the largest credit card processors in the world, Fiserv, which also has a solid product line of hardware equipment to meet the needs of any type of business, regardless of how old or new.


Other areas that merchants often should evaluate payment processors on, given their history, is to check how well a processor has adapted to the changing FinTech landscape. Digital wallets were still in their infancy 20 years ago with the advent of eCommerce and PayPal. That payment method is expected to cross 53% of all eCommerce by 2025] . As consumers grow more comfortable with online and digital payment tools and with business being conducted at close to real-time speed, how well-equipped is a payment processor to meet the needs of merchants in these changing times? As security precautions increasingly swarm the conversation about transactions, given the speed and sophisticated methods of the flow of money, is the payment processor staying abreast of all the changes? We look into these questions and much more in this review of Flagship Merchant Services.


The company offers credit card processing solutions across traditional, virtual, and mobile platforms and has partnered with Clover to provide equipment to process payments. Although Flagship markets its products as simplifying PCI compliance, the company does not offer any PCI-compliance consultation to help merchants become more compliant. Retail and restaurant businesses are advertised as the target market for Flagship’s payment processing solutions, although the company also supports eCommerce platforms via Flagship’s payment gateway and virtual terminal solutions.


In addition to standard credit and debit card processing services, Flagship offers a free mobile app that can be used as a virtual terminal for on-the-go transactions. The app allows business owners to quickly run and view reports, oversee sales transactions, and manage financial statements. Flagship also offers a lending facility such as the same-day funding program. The company offers other ancillary services to help merchants. Flagship offers Pirq, a solution for businesses to address their marketing needs by setting up loyalty rewards for their customers.


Although details on processing fees and scalability are not readily available on the company’s website, Flagship offers payment processing via Fiserv and PaySafe, enabling the company to provide various services and options to merchants of varying sizes based on transaction volumes. Flagship provides support in-house to get merchants properly onboarded to set up and configure a point-of-sale solution and sufficiently trained on the company’s service solutions.

Flagship History and Founder

Flagship Merchants Services has been operating since 2001, since its founding in Charlestown, Massachusetts. Paysafe acquired the company, and Nathanial Short is currently overseeing the operations of the company. 

What Is Flagship Best At?

There are many different types of industries that Flagship caters to. The eCommerce industry is a clientele that Flagship targets, as are various types of food businesses, such as restaurants. Retailers are another merchant type that can use Flagship’s services as it also specializes in catering to them. Over the years, these industries have become intertwined in the kind of payment processing needed for their businesses.


For example, an eCommerce business in the past needed a payment solution for online transactions. There was the question of what services did a payment processor offer to address the needs of merchants in all areas of an online transaction cycle; a website, a shopping cart, a virtual terminal, a payment gateway, 3D Secure, chargeback protection and consultancy, etc. Today, such solutions are just as important to food services and brick-and-mortar retail businesses, as online shopping permeates these industries just as the in-store experience does.



As a result, all these businesses can benefit from various equipment available through any of Flagship’s partners, whether a traditional or wireless POS that can process EMV or contactless payments or using an app, such as ROAM, offered by the company. As always, all businesses can now have an online presence and seamless process payments because the company partners with the payment processing industry’s de facto standard of payment gateways, Authorize.Net.

Flagship Products and Services

Flagship offers merchants diverse solutions, including payment processing, mobile and traditional point of sale solutions, and additional services such as integrations, eCommerce options, merchant cash advances, and analytics-related features. Below is a highlight of some of the company’s service offerings.



Payment Processing – In today’s economic climate, it is crucial for businesses to accept all major credit cards. The company provides businesses with a processing solution that meets the merchant’s and their customers’ needs. While Flagship’s credit processing solutions are advertised as ideal for brick-and-mortar merchants in the retail and restaurant industries, the company also offers eCommerce and virtual terminal solutions. Flagship’s accepted payment methods include swipe, EMV, contactless, and mobile. 

Point of Sale and Mobile Apps

Point of Sale terminals – Flagship Merchant Services’ credit card processing solution, in partnership with Fiserv and Paysafe, can handle various transaction volumes. Still, details can only be obtained by contacting a representative. Their online form for further information does provide a breakdown of monthly processing volume into three categories: Under $1,000, Between $1,000-$10,000, and over $10,000. All of the company’s point of sale terminals are EMV and NFC compliant.


The company offers a range of hardware options, primarily Clover-based devices such as the Clover Flex, Clover Station, Clover Mini, and Clover Go, with features such as EMV, NFC, PIN code, and swipe payments. Clover Station offers over 200 apps, including a customer database, sales, team member management, and inventory. MobilePay, an option outside of Clover-based devices, is also available through the iPayment mobile app.


Flagship’s support team assists businesses in setting up and configuring their POS solutions properly. They offer training by working with a representative or calling their customer service support number.


Mobile POS – Flagship offers a free mobile app that functions as a virtual terminal, allowing business owners to conduct transactions on the go. This virtual terminal will enable owners to run and view reports, monitor sales transactions, and manage financial statements. In addition, the merchant console allows for establishing user permissions within the virtual terminal.



In continuing its strategy of building strong channel partnerships with world-class leaders of product domains, Flagship partners with iPayment to offer the company’s MobilePay suite of products and services for MPOS. 

Tertiary Services Include:

Lending services available through Flagship: lending activities available through a payment processor are ubiquitous nowadays. The availability of such a product can be a win-win for merchants and merchant service providers. The merchant has seamless access to credit without the lengthy wait times or convoluted application processes they’d be subject to via traditional lending channels, such as banks. The payment processor can quickly gauge the right amount of credit risk and creditworthiness of a merchant, given their history and transaction volume with the payment processor.


Flagship Dashboard and Analytics – Although an analytics and dashboard tool such as iAccess is now offered as a standard feature by most merchant account providers, it’s still reassuring to see that the cloud-based analytics and reporting tool is included for Flagship customers. This tool is ideal for monitoring the business effectively.



Flagship Gift Card and Loyalty Program Solutions – Pirq is a Flagship partner that allows merchants to set up gift cards and loyalty programs for their customers.

The Company’s Pricing and Fees

The rates and fees for Flagship merchant accounts can differ depending on a range of factors, such as the type of business a merchant operates, their processing volume, and the agent responsible for setting up their account. While Flagship usually offers a month-to-month contract that doesn’t involve cancellation fees, some Flagship Merchant Services reviews indicate that such costs exist.


Flagship mentions that they have no annual or monthly fee for their service. However, the company charges a PCI Compliance fee of $99 annually. Furthermore, some customers complained about a $29.99 monthly fee for affiliate marketing through Womply, a company that Flagship works with. Some business owners have reported being automatically enrolled in a free 60-day Womply trial in late 2016, and those who opted out after the trial ended were subsequently charged $29.99 per month.


To offer a payments gateway and a virtual terminal, Flagship partners with, which does post its transaction fees. There is no setup cost for, and its advertised plans offer a monthly payment gateway for $25. There is an All-in-one plan, which charges 2.9% + $0.30 per transaction. The Payment Gateway-Only plan also charges a flat rate of $0.10 per transaction plus an additional $0.10 daily batch fee.


The hardware cost is not disclosed on the company’s website, but Flagship does provide a complimentary terminal with any contract. However, returning the equipment may incur extra charges if the agreement is terminated. The equipment packaging must be unopened in its original packaging, and the business must return it within 30 days of the purchase at their own expense. Additionally, the merchant may face a restocking fee between 15% and 25%.


There needs to be more information on per-transaction costs or specific software and licensing fees on Flagship’s website, making it impossible to compare the company to other credit card processors in our ratings. Instead, Flagship encourages new and existing customers to contact their sales team for detailed information on processing fees and hardware costs.


There is a company guarantee that If Flagship fails to provide the lowest total processing cost, the company will offer the business a $200 American Express gift card. Additionally, Flagship’s refer-a-merchant program rewards successful referrals with $100. However, given the lack of transparency regarding fees and hardware pricing, it is nearly impossible for businesses to research costs independently without first speaking to a sales representative.


Before signing up, merchants must thoroughly read and comprehend Flagship’s merchant account agreement. Carefully review for undisclosed fees or rates that are higher than anticipated. Flagship can provide interchange-plus pricing, and although the company does not seem to promote it proactively, merchants should also consider that option.


Although Flagship has a Rates & Fees page on its website, it needs to provide concrete information on rates or fees. Instead, the page contains marketing fluff about the company’s guarantee to beat competitor rates.


It is highly recommended that business owners thoroughly read and comprehend Flagship’s merchant account agreement before signing up. Like many other providers, Flagship uses multiple pricing structures, and often, unbeknownst to merchants, payment processors offer the plan most suitable to their bottom line. Interchange pass-through pricing plan is much more transparent and, most often, financially viable for businesses.


Since the company offers pricing via a sales rep and pricing-guarantee option, it’s recommended that to simplify the process of comparing rates and fees with other processors that merchants are considering, they can quickly request a quote from Flagship through this profile. That process is quick, free, and non-binding, giving business owners a clear idea of how Flagship Merchant Services’ pricing measures up. To begin, simply access the quote comparison form.



We have found alternative reviews for the company’s interchange plus pricing based on customer feedback. These reviews mentioned that Flagship’s interchange plus pricing is very competitive, and it is unfortunate that the company does not market this pricing structure more openly. Of course, it’s important to note that the rate available to any merchant can only be determined on their own merits, on a case-by-case basis.

Details Of The Contract Offered and Customer Service Details of Flagship

Flagship Merchant Services provides month-to-month contracts without early termination fees. The company offers a 24/7 customer and technical support line and a dedicated website for approved merchants to review transactions, run reports, or download statements.


Previously, merchant accounts came with long-term contracts and early termination fees. However, due to technology companies that have entered the fray over the past decade, such as Square and Stripe, to disrupt Financial Technology, such contract arrangements are becoming less and less common. Flagship offers some freebies to discourage merchants from closing their accounts, but it has limitations. Merchants can only receive one cheap terminal, which must be returned promptly if the account is closed.



Additionally, a long-term contract with an early termination fee is required, and merchants have reported difficulties canceling their accounts. As a result, buying processing equipment outright and sticking to month-to-month billing is generally the ideal option for merchants considering Flagship Merchant Services as their payment processor.

Are There Any Complaints About Flagship?

One of the biggest mainstays of payment processing services to a business is the level of support offered. It sounds obvious, given that the merchant service provider will be responsible for getting businesses their money promptly without any surprises. And if there are surprises, the payment processor proactively addresses any merchant concerns. Although Flagship offers around-the-clock multi-channel customer support, it isn’t always easy to get in touch with someone at the company.


It should be noted that there have been complaints on multiple online forums, other review platforms, as well as the Better Business Bureau that the account manager was available only sometimes, and issues involving transactions or account holds may need to be resolved by Fiserv and not Flagship.


Common issues highlighted by the complaints include funding holds, “hidden” fees, poor customer service after sign-up, and difficulty canceling service. While some of these issues are beyond Flagship’s control, they could better communicate more proactively with merchants around issues related to funding holds.



Additionally, sales agents could be more transparent about what merchants will be charged for. There have also been complaints about merchants being unable to get through to the company’s designated account manager or the support team to resolve their issues. Finally, some merchants have had difficulty canceling their service, and Flagship should promptly refund any fees charged on any services that merchants have not or are not using. 

Customer Support

From experience and the reviews left by the users of Payment Depot, this merchant service provider supports its customers via:

24/7 Help & Support

Not available

Phone Support

Not available


Contact Form Available for Existing Merchants for Troubleshooting


Basic FAQ Online Help Page


Overall, the company is a decent option for merchant services. Flagstar offers a range of payment processing solutions that cater to the needs of small and medium-sized businesses. The company provides payment processing services across traditional, virtual, and mobile platforms and has partnered with Clover to offer point of sale hardware devices and solutions.


Unfortunately, the company does not offer any type of PCI-compliance consultation to help merchants become more compliant, which is surprising since it is that compliances that is the underlying bedrock of their marketing efforts. The company’s services include payment processing, mobile and traditional point of sale solutions, and additional services such as integrations, eCommerce options, merchant cash advances, and analytics-related features.



The company charges no monthly or annual fee but charges a PCI Compliance fee of $99 annually. While the rates and fees for Flagship merchant accounts can differ depending on various factors, Flagship usually offers a month-to-month contract that doesn’t involve cancellation fees. Since the company does not disclose rates on its website and simultaneously offers to beat competitor pricing, we recommend that merchants negotiate hard to secure the best pricing available from the company.