MD HQ allows you to process credit card transactions and recurring subscription payments via your Stripe account. The EMR communicates with Stripe via an API, meaning that once you set up your Stripe account and we connect to it, you continue to handle billing inside MD HQ, rather than having to go to an external website or application.

This help section describes how you set up and connect your Stripe account to begin processing credit cards via the EMR and Patient Portal.

Setting Up Your Stripe Account

First, set up your account at Then activate your account (use the link or, from your Stripe home page, click on "Your Account" in the upper righthand corner and then on "Activate Account"). You will need to provide basic information about your business and the bank account where you want credit card payments to be deposited.

Stripe Screenshot - Activate Account

Toggle into Live mode by clicking the toggle button in the upper left hand corner of your Stripe dashboard. You can go back to Test mode at any time, but can only process credit card payments in Live mode.

Linking Stripe to MD HQ

Go to your Stripe Account Settings (use the link or, from your Stripe dashboard, click on "Your Account" in the upper righthand corner, then click on "Account Settings").

Get your API Keys: Under the Developers Tab you will find the API keys, copy and paste both live API keys (not the test keys) into a sticky note on the schedule home page of your EMR. The two keys, which are long strings of letters and numbers, should start with "sk_live_..." and "pk_live_..." Send us a note at to let us know when this is done. We'll log in to your build, pick up the keys, and use them to connect your Stripe account with your EMR build. Note: DO NOT send us your keys via email, as this is sensitive information and email is not secure.

Configure Webhooks: This is optional, but strongly recommended, particularly if you use subscription billing. Webhooks allow our server to log what Stripe is doing so that we can alert you if there is a failed payment, for example, or help look through the logs if you think there has been an error. Otherwise, we have no way of seeing what Stripe is doing. Note that sensitive information (like a credit card number) is never viewable or logged by our system.

Configure webhooks by clicking on the webhooks tab and then on "+ Add endpoint." Type in https://YOUR EMR, replacing YOUR EMR URL with the actual URL of your EMR - see below for help with this. Don't forget to include the /webhooks/stripe.php part at the end!

  • What is my EMR URL? Looking at any page of your EMR, copy everything in the web address bar between "https://" and "". So, for example, if you see "," the text you are looking for is: "demo1".

Stripe Configuration Options

You can set various configuration options for Stripe in the "Your Account" pop up window, including:

  • In the main tab - check the box if you want a credit card payment to be declined if there is a mismatch with the zip code or the CCV.
  • In the subscriptions tab - tell Stripe what to do if there is a failed credit card payment. The default is for Stripe to retry three times, but you can vary this, as well as set the interval at which it should retry each time.
  • In the emails tab - set whether Stripe sends you and/or your customer an automatic email when a payment is made and customize your Stripe invoices.


When setting up your subscription options in Stripe, you will want to make sure to set your options correctly for failed subscription payments. Specifically, set the desired retry options, and under the "Then finally" drop down menu, select "leave the subscription as-is." This means that the subscription will continue to run and try to pay using the then-current payment information on file for that patient, and generating a failure notice within the EMR if the payment ultimately fails. DO NOT select "mark the subscription as unpaid." If this is selected, Stripe may stop trying to pay the subscription without sending any failure notification of any kind.

Accepting FSA and HSA Cards on Stripe

Stripe is able to accept Flexible Spending Account (FSA) and Health Saving Account (HSA) credit/debit cards. However, before you can do so, you need to contact Stripe and request that they classify your account as an MCC business. More information on setting this up can be found here:

Getting Credit Card Information

If you have credit card information on file in another program, such as or Braintree, Stripe can likely import this information. Or you can add a credit card to a patient's account in the EMR by clicking on "Save New Credit Card" in the Billing Info tab of the Patient Info pop-out. Or, patients can add a credit card via their Patient Portal account if you have this feature turned on. Contact if you would like to activate this feature.