Flagship Merchant Services review

A flexible offering that's especially good for big companies: read our Flagship Merchant Services review to find out more

Top Ten Reviews Verdict

Flagship Merchant Services offers flexible plans for different types of merchants with no setup or termination costs. Be wary of hidden fees, and ask plenty of questions when signing up.


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    No setup or termination fee

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    Flexible, monthly terms


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    Monthly minimum volume

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    Annual PCI compliance fee

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Flagship Merchant Services: Key specs

- Secure payment gateway and virtual terminal
- Real-time payment processing
- Sales tracking and reporting
- Shopping cart setup
- Hardware and POS software
- Fraud prevention
- Merchant console
- PCI/DSS compliance
- Business management portal
- Gift cards and loyalty programs
- 24/7 customer support
- Simple-to-use payment buttons
- Merchant account setup

We voted Flagship Merchant Services as the number-one, best credit card processing services for eight years in a row between 2008 to 2015, and with good reason. One of the first payment-processing providers to offer free setup and month-to-month contracts with no early termination fee, it quickly acquired a large, loyal fan-base. 

The company offers free gateway setup with Authorize.net (usually $49) and a free shopping cart for ecommerce customers. It can supply a free mPOS app and card reader as well. For retailers, it offers a free credit card terminal, or will re-program existing terminals.

In 2012 Flagship Merchant Services merged with its processor, iPayment, and has definitely had its ups and downs since, especially when it comes to customer support. However, it still has a competitive offering for larger-volume customers including no higher charge for American Express processing.

Flagship Merchant Services review: Features

  • Good quality hardware options for purchase
  • Competitive pricing with no higher rate for American Express
  • Telephone and mail order solutions

For those merchants who want to accept phone and mail order transactions, Flagship Merchant Services will set you up with a merchant account and virtual terminal. This does take time, which can be frustrating when competitors like Stripe Payments and Square Payment Processing are able to bypass this process completely. 

However, having a merchant account allows you to accept payments in multiple currencies, a wider variety of cards and offers increased security to combat fraud.

Flagship Merchant Services has partnered with Clover POS systems to offer a full range of high quality hardware for bricks and mortar retailers and restaurateurs. 

Clover is a highly-rated, affordable, user-friendly POS system provider with lots of customizable options so this is definitely a great selling point. If you already have hardware you are happy with, Flagship will reprogram them for use with its payment-processing system. 

It also offers a mobile card reader and mPOS app through iPayment. It doesn’t accept contactless payments, but it is compatible with both Android and iOS.

For eCommerce-only customers, Flagship Merchant Services offers an elegant solution that includes the Authorize.net payment gateway and central portal to manage the account, and some really smart fraud detection tech that is fully compliant. 

The company does offer API developer tools to customize your checkout and/or integrate with a shopping cart, but the ‘buy now’ buttons are easy to embed into your site with a simple copy and paste HTML code, with no developer required.

One of the selling points of Flagship Merchant Services is that it doesn’t charge any extra fees for processing American Express. Amex has long been the problem child for merchants, caught between its attractive, affluent customer base and the fact  the business model involves charging merchants disproportionately high fees compared to Visa and MasterCard. 

If your business has a high average ticket price, then there is also a good chance many of your customers are paying with American Express – and so using Flagship Merchant Services could be very beneficial.

When it comes to pricing specifics, Flagship Merchant Services is not transparent at all. The only advertised rate published on the site, 0.38%+19c, is a deceptively low rate for debit card transactions. 

Even when you get to speak to the sales team, they will not open up about their pricing across the board. They say this is because they offer ‘tailored rates’ to suit ‘unique business needs’ which does make you feel a bit like you are bartering at the souk but also gives you a chance to negotiate the best deal for your business. If you don’t feel comfortable with that, then Dharma Merchant Services might be a better solution. 

That’s a traditional payment processor like Flagship, but publishes all its rates upfront including its very competitive Amex pricing. Flagship does offer a choice between tiered pricing and interchange plus – we recommend the latter for best value.

Flagship Merchant Services also offers a Merchant Cash Advance of up to $150,000 paid back through a cut of your daily credit card processing. While it’s a great service to offer, make sure you understand the rates at which you are paying back this loan as you could find your cash flow compromised.

Flagship Merchant Services

(Image credit: Flagship Merchant Services)

Flagship Merchant Services review: Usability

  • Personal, tailored service
  • Modern virtual terminal with third-party provider

The setup process is a little bit cumbersome, with no web-based portal like Square, Stripe or even PayPal for Business. Instead, you fill out an online form and a sales rep will give you a call. This is your opportunity to ask all the questions you need to know the answer to, and negotiate your rate – the type of personal service that has become the exception to the rule. 

You can definitely take advantage of this by drilling down on the transaction rates offered to get the best possible deal for your business, something that is simply impossible to do with completely web-based services. Make sure you do your research so you can compare the rates offered to the industry standard.

This is also the point in the process that seems to generate most complaints about Flagship Merchant Services. While it is very keen to tell you about the fees it doesn’t charge, it’s not so upfront about what it does bill you for, leaving some merchants with a bad taste in their mouths. 

Flagship Merchant Services does have a monthly fee, and requires a minimum monthly volume of $25 – although seasonal businesses can negotiate a hiatus. It also charges you a small monthly amount for your payment gateway. Some of the fees, like PCI compliance, are annual, so although there are no penalties for early termination you will lose these upfront charges.

Once your application has been accepted and your merchant account opened, you will be furnished with an Authorize.net payment gateway to integrate into your website, and a virtual terminal for eCommerce users. 

This means your business portal is actually run by a third-party provider, not Flagship itself. If you require a shopping cart you will need to source that through a third-party integration. Mobile payments are via iPayment and accounting is through QuickBooks. 

While third-party integrations are common, to have your account portal hosted by a third-party provider may make some users feel uncomfortable, and restricts functionality to some extent. The upside is that Flagship offers full support with setup for those with no prior experience or knowledge.

The Authorize.net virtual terminal doesn’t offer the most visually appealing design, but it is fairly straightforward in terms of usability. The left hand side of the dashboard offers you simple short cuts for uploading transactions, setting up recurring billing, QuickBooks integration and more. 

Across the top of the dashboard are tabs that will take you to your tools, your reports, to a useful transaction search function and to your account information settings. Authorize.net also offers a verified merchant seal to display on your website to add to consumer confidence around security.

Flagship Merchant Services review: Performance

  • Company-wide reporting system for customer contact
  • Tailored plans for specific businesses
  • Customer loyalty scheme

Flagship Merchant Services has come under criticism for its customer service in the past, especially around contract termination. Although it was one of the first companies to implement a 24/7 helpdesk, this team is only partially based in-house and service levels were extremely variable. 

However, the market spoke and the company listened – in 2014 it instigated a company-wide reporting system for customer contact. If you speak to anyone, in any department at Flagship, about any issue at any time, they record it so contact is easily traceable and can be followed up.

As well as tailored pricing for your business, Flagship Merchant Services offers different integration packages depending on what type of merchant you are. For example, the ecommerce package offers credit card processing, online payments and processing, advanced fraud prevention tools, API developer tools, an ePayment button with simple HTML cut and paste coding, and a virtual terminal. 

The phone and mail order package adds customer management and recurrent billing as well as a merchant account for payment processing. If you are a retailer or restaurateur, you can add hardware options. 

The digital loyalty program, Pirq, is an attractive add-on for retail and hospitality. It is presented as a free app your customers can download to their smartphones, which acts like a digital punch card. All your customers need to do is scan your merchant tag at the checkout to earn loyalty points. 

In exchange for rewards, customers allow Pirq to track their purchasing habits and Pirq provides you with information to help customize and improve your offering. Pirq has also been shown to actively drive sales in its own right.

Flagship Merchant Services review: should you buy?

Most of the major selling points of Flagship Merchant Services, such as no setup costs, monthly contracts and no termination fees, are now offered by the majority of major competitors. It was once ahead of its time but it seems to have stagnated in this area a little. 

Coupled with a lack of transparency over fees and a mediocre customer service record, smaller volume merchants may well find better solutions with the likes of Square and Helcim.

That said, Flagship Merchant Services still has a lot to offer, especially for merchants who like the personal touch. The hands-off setup, with no need to bring a developer, means that even those with limited experience of content management systems and software as a service can get the most out of Flagship and its integrations without having to pay a developer. 

If you do have a developer to hand, there are some customizable solutions as well – but nowhere near as flexible as the Stripe platform. While the absence of published pricing may ring alarm bells for some, Flagship does offer a service that is tailored to your business, and many merchants might like the opportunity to be guided through integrations and negotiate rates with a human being.

Integrations are offered with trusted partners like Authorize.net, QuickBooks and iPayments, giving you peace of mind over the quality of the service being offered. All these options have some level of customization as well, some of which does not require developer involvement. While the upfront charge for PCI compliance is no longer usual, it does guarantee that you are meeting your legal obligations without any ambiguity.

Flagship’s pricing structure is one of the least transparent on the market, but this does give you a chance to negotiate with your sales adviser to get the best deal. If you aren’t comfortable with that, then you may prefer Dharma Merchant Services – a traditional processing service with a very upfront proving structure.

There are many nice touches to Flagship Merchant Services, such as the loyalty program, but this is one credit card processor it is hard for a third party to recommend. Because it offers so many different levels of service and functionality, it is best to school yourself on the options available, and then give them a call. A good understanding of your own business needs coupled with an awareness of competitor rates and services should help you get a good outcome.

While many credit card payment processors are moving toward an online building blocks model of service that streamlines the merchant experience, fees and timeframes involved, Flagship Merchant Services still offers a more traditional sales-based approach that is no doubt very welcome among some sectors of the merchant community.

What other credit card payment services should you consider?

Flagship Merchant Services is one of the best credit card processing services but it might not be the right one for you business. As you would expect, there are plenty of other services for you to choose from. Here are the ones we think are worth consideration and what they're most suitable for; click through for the full review.

Helcim is a great all-round option; Stripe Payments offers great customisation options; Fattmerchant is good for large volume; Dharma Merchant Services is an ethical business option; Square is best for SMBs; PayPal Business is best for micro-businesses; and iPayTotal is the best for high risk merchants. 

To see all these compared in once place, read our Best credit card processing service buying guide.

Looking for pricing information on credit card processing services? Answer the questions below, and our vendor partners will contact you with a free quote: 

Jai Breitnauer

Jai Breitnauer writes regularly for a variety of business and consumer publications including NZ Retail magazine and Idealog, the home of business innovation in Aotearoa. She has edited books about accounting and business journals for the optics industry. She works for Top Ten Reviews by doing reviews of chainsaws and other garden equipment.