Practice Management Small Business Tech Trends

Merchant Services-Intuit and Beyond

Written by Jim Savage

Is it just me, or is merchant account processing way more complicated than it needs to be? Take for example, Intuit Merchant Services. If you look on their website at, you will see the following account options:

  • Intuit Online Terminal
  • Intuit Go Payment
  • Intuit Merchant Service for QuickBooks
  • Intuit Merchant Service for Web Stores
  • Intuit QuickBooks Point of Sale Merchant Service
  • Check Processing Solutions
  • Intuit Payment Network

That is 7 different ways to get paid, and this is just one credit card processor! Could they make it any more confusing? Couldn’t they just make it one account with 7 options? Since we are talking about web stores for this article, we will only discuss Intuit Merchant Service for Web Stores and Intuit Merchant Services for QuickBooks. We’ll look at how to integrate these into your eCommerce strategy, and take a look at some other options if Intuit doesn’t fit with your strategy.

In discussing merchant accounts, it is important to clarify the difference between a merchant services account and a payment gateway.

Merchant Services

Merchant Services to process credit cardsIn order to process credit/debit cards, you will need a merchant service account. A merchant service account is a type of bank account that allows businesses to accept payments by debit or credit cards. So a merchant account is an agreement between a retailer, a merchant bank and payment processor for the settlement of credit card and/or debit card transactions. The merchant account is established under an agreement between an acceptor (person accepting the credit card) and a merchant acquiring bank for the settlement of credit card and/or debit card transactions. Whether a merchant enters into a merchant agreement directly with an acquiring bank, or through an aggregator such as PayPal, the agreement binds the merchant to obey the Operating Regulations established by the card brands.

Examples of merchant service providers are Intuit, Bank of America and Wells Fargo. Merchant service providers can offer an actual stand-alone piece of equipment residing at the merchant site where a card can be scanned or the number can be entered into a terminal. They can also work directly within a web site shopping cart. This terminal, or virtual terminal, contacts the card provider through a payment gateway.

Payment Gateway

Payment GatewayA payment gateway is an eCommerce service that authorizes payments for e-businesses and online retailers. This service uses encryption to securely send credit card data to a merchant account provider. It is the equivalent of a physical POS (point-of-sale) terminal located in most retail outlets. A merchant account provider is typically a separate company from the payment gateway. Some merchant account providers have their own payment gateways, but the majority of companies use 3rd party payment gateways. The gateway can work two ways:

  1. The virtual terminal that can allow for a merchant to securely login and key in credit card numbers.
  2. The website’s shopping-cart can connect to the gateway via an API (Application Programming Interface) to allow for real time processing from the merchant’s website.

Examples of payment gateways are and Intuit also acts as a payment gateway for some shopping carts.

Intuit Merchant Services for Web Stores

I’ve recently discussed shopping carts, so with which shopping carts does Intuit Merchant Services integrate? Actually, only a few. According to the web site, as of this writing, it works with:

So, what if you are using another shopping cart and you want to use your Intuit Merchant Service account? You have a few options:

  1. Hire someone to develop a custom interface to connect your shopping cart to Intuit Merchant Services. This will require someone with knowledge of the SDK (Software Development Kit) for Intuit Merchant Services. Not an easy task, yet certainly can be done.
  2. Use a merchant account/payment gateway other than Intuit. The most widely used payment gateway is For a list of merchant service providers that work with you’ll want to look at the Authorize.Net reseller directory For compatible shopping carts look at the Authorize.Net Certified Solution Directory. The downside to this option is the lack of QuickBooks integration. However, a third-party application, such as eCC or T-Hub, can integrate with most of the major shopping carts. See our  article on shopping carts for more information on this subject.
  3. If neither of these options work, as a last resort, you can switch shopping carts. This is the least preferred option.

Whichever path you choose, be sure you do your homework and choose the right components to fit your situation. Regardless of which merchant service solution you choose, one of the biggest challenges with merchant accounts and Quickbooks is reconciling your bank account and accounting for the fees.

Merchant Account Reconciliation

Reconciling your Merchant AccountOnce you have the merchant account setup and your data is flowing into QuickBooks, you still face the tedious chore of reconciling the merchant account payments to your bank account. The biggest advantage to using Intuit Merchant Services for QuickBooks is the built-in tools in QuickBooks and the tight integration. If you are using another merchant service, reconciling your merchant account can be very time-consuming and frustrating. This is mainly due to the fact that a lot of merchant accounts take out their discount fee before depositing your funds into your checking account, so the amount you have in Undeposited Funds never matches up to your deposits. Also, payments processed on one day may show up on the next day’s deposit, making it difficult to match the bank deposits to the actual transactions. Some people simply enter the difference between the sales and actual deposits as the merchant account fee, but this is not a true reconciliation and you run the risk of transactions “falling through the cracks” and not getting all the money you have coming.

Some merchant services providers will do what is referred to as “gross daily settlement”. With this method, the gross sales will be deposited into your account, making it much easier to match to your sales. At the end of the month, they will debit your account for all of the fees in one lump sum. This makes reconciliation much easier, you just need to make sure you leave enough money in your account to cover the fees.

Merchant account reconciliation can be one of the most frustrating aspects of having an eCommerce store. Make sure you develop a system early on and stick to it.

About the author

Jim Savage

Jim Savage has been a QuickBooks Pro Advisor since 1999. He has since signed on with the Intuit Solution Provider program, which specializes in marketing to the mid-market channel. In addition, he is an Advanced Certified Pro Advisor and his company, Savage and Associates, is an Advanced Certified Pro Advisor and certified in QuickBooks Enterprise and QuickBase in the ISP channel. Prior to becoming a Pro Advisor, Jim was an IT director for a major health insurance carrier and has been involved in large scale IT projects throughout his career. He is now specializing in EDI and E Commerce clients and integration with QuickBooks. Since he has referred to himself as "The QuickBooks Guy" since he started, his website is named appropriately,


  • Hi, I use Intuit Merchant Services for processing credit card statements. I wonder if any other users are able to reconcile their statement? I have found that the charges listed on their monthly statements and what they take out of my checking account do not line up. The charges are frequently lumped together when taken out of the checking account, and not so on the statement, and to further complicate things, when I download the daily charges, they are in yet even a different order. When we try to reconcile our checking account, what we have downloaded, doesn’t line up with what they then actually debit my checking for. In other words, if I download 3 charges for $10.00 each, and it is automatically entered into my checking that way, when the bank statement comes, they have made a single debit for $30.00. Try and reconcile that!
    Other than that I am very happy with Intuit Merchant Services

    • Joslyn, It has been my experience that reconciliation is the most difficult part of all of this, whether it is with Intuit or another merchant service. The more volume you are doing, the more complicated it becomes.

    • Joslyn / Jim,

      I am not sure if you know this or not, but when Intuit sets up a merchant account, the default setup is to have the fees deducted from every deposit. This make reconciling much more time consuming. The preferred method is to have the merchant fees and discounts deducted separately from your bank account as a separate fee as a lump sum total only once a month. As Jim stated, this is known as the “Gross Daily Settlement”. What most people don’t realize is that a merchant can request Intuit to switch their settlement method from the fees being deducted from each settlement to the “Gross Daily Settlement” method. I have done this for my own merchant account as well as for my clients who use Intuit Merchant Services. What a difference it makes. Try it, you’ll like it.

      • Danny,
        Thanks for this. I couldn’t agree more about how this Gross Daily Settlement method simplifies bank reconciliation and overall complexity. Everyone should elect to switch, and it’s a bummer that Intuit’s default is to deducte fees from each sale.

      • I just set up my merchant account and had huge problems with fixing errors in the initial setup which had been done with QuickBooks over the phone. Quite a number of things were set up incorrectly and it took hours on the phone to fix. I would love to change to the “Gross Daily Settlement” settlement method, but can’t see a way to change it online, would that be possible, rather than calling?

        • Cat,

          I don’t believe there is a way to do this online. I believe you will have to call.


          • Before reconciling, go to home page and click merchant service deposits, this will take you to Deposits and fees screen, just unclick the transactions fees.And then I use my bank statement to apply whatever fees where incurred. Hope this helps

  • Jim,
    Merchant Account Reconciliation hasn’t been very good lately if you have IE9 installed. I’m using QB Premier Accountant 2010 R14. Merchant Services Deposits fails to complete. It’s a known issue and the only advice is to uninstall IE9. The workaround that I discovered is to use the normal Record Deposits, as we did pre-2010. We can’t access Merchant Services statements from within QB which meant that we had no record of fees that were charged, making reconcilliation a joke. During a particularly long and frustrating tech support call, I finally requested a password so that I could access my account using Firefox. They didn’t think that Firefox would work but it did! The primary reason for using Merchant Services is no longer particularly valid.

    • I have noticed the issue you are talking about with IE9, which frequently hangs. I have switched almost everything over to using Chrome and am very happy. Some things still require IE, so I still keep it around.

        • That is one of the things that I referred to for keeping IE around, it is built in to QuickBooks and some other Intuit functions.

      • The only thing that ever hung in IE9 was having QB download the deposits and fees. That would hang every time. I could process credit cards with no problem. The hanging was fixed for a couple of weeks and then broke again not too long ago. I finally uninstalled IE9 which reverts you back to IE8 which QB likes better. But, I’m a web designer. I had IE9 installed because it is much more web standards compliant than IE8. IE9 is very close to surpassing any of the earlier IEs as far as browser usage is concerned. It’s a browser that I can’t ignore. It is very telling that QB is so slow in adapting to the changing face of the web.

  • I use merchant services for 2 of my business. One is a retail business. The other is service business. I have no problems with reconcilation of my statements. They always match up exactly. That said I usually only have 1-2 CC transactions a day. So maybe it is because my volume is low. I have never encountered any errors. I have used Merchant services with Versions 2009, 2010, 2011 and 2012. I have several bookkeeping clients that also use 2010 with no problems.

    • R Neilson, yes, when volume increases, you’re bound to have challenges with reconciliation. The timing of deposits, the batching, the credits, etc. tend to make reconciliation very challenging when you have hundreds of transactions per week. Also, if you have multiple points of entry such as a web store (or two in our case), plus phone orders, you might have multiple batches coming from different places. It gets difficult and QuickBooks reconciliation tools don’t really do the job.

  • Pro Advisors should note that if Jim’s option #2 (using as the gateway provider) is used, Pro Advisors discounts do not apply. I have a client using Intuit Merchant Services with and it is going ok but he had to negotiate his own fees and I couldn’t pass any of my discounts on to my client as part of the PA program.

    • Kathie raises a good point. For those of us who resell Intuit Merchant Service, recommending something other than Intuit can have monetary implications. But there are situations where Intuit may not be the best fit.

  • What do you think of B of A’s Skipjack add on to make their system work? B of A cost is less than Intuit. Thank you!

  • Hi Jim – I have been trying for days to get straight answers from and Inuit on integrating the two. I get so many different answers from them.

    The most positive answer is that I get an account, make sure it is the Omaha location, link it to my Inuit merchant services account, and link this as a new account into QuickBooks. Transactions (batches) will start coming in.

    I am now being told by Inuit Payment Solutions that this is not true. They will resell me an account, but not only will it not connect to my existing Inuit Merchant account, but will be a new one that won’t be able to get transactions down into QuickBooks.

    I am so frustrated, I am wondering for the transactions I will have (10 a week) for the first year, I might be better off keeping track of things via a spreadsheet and managing everything from portal. I was hoping to just give my accountant the QB file at the end of the year, since I have other revenue streams and expenses, would be easier. But seems like it would be easier for them, and if not impossible for me them challenging.

    What is the real story here and what advice would you have? Thank you…

    • Terry,

      Pretty confusing huh? You can get an gateway through Intuit, most of the reps at Intuit do not know about it. You may want to check out Mercury Payment Systems, the rates are better and the integration with QB is better. Feel free to contact me off post and I can refer you to the right person.

      [email protected]

  • Is there an automated interface between other Merchant Account providers or do you need to use Intuit? We use Wells Fargo but need to manually reconcile between our eCommerce store (Network Solutions) and Quickbooks.