Processing a Payment

Let’s review how to collect a credit card payment in the EMR. To collect payments, you must have already completed the setup process outlined here.

There are three types of payment entry:

  • Card-present (CP): Transactions represent credit card purchases that involve the presentation of a physical credit card by the customer to the merchant.
  • Card-not-present (CNP): Transactions in which a merchant honors the account number associated with a card account without the physical card being present.
  • Card-on-file (COF): Transactions paid by a card that was tokenized during a previous transaction.


We’ll detail each step in the payment collection process while highlighting the variations between the different types of payment entry. Patient payments can be collected directly from the appointment or through the patient’s chart.

Important: You will never type in credit card information using your keyboard, as this is not encrypted. By using the provided device to key in the credit card information, you’ll ensure that your patient’s information remains safe. Alternatively, you can limit your use of the provided device for future transactions by taking advantage of the card-on-file feature.

Processing a Payment

Patient payments can be collected directly from the patient’s appointment or through the patient payment section of the patient’s chart. If you are taking payments for multiple or past Dates of Service, we recommend entering these via the patient chart. In this example, we’ll collect the payment through the appointment.

  1. Navigate to the patient’s appointment in the Scheduler, and click to open.
  2. Click Check In. The Payment window will automatically open if the patient has a copayment or coinsurance on their chart. Otherwise, you can click Payment to add a charge.
  3. Once all charges have been added, click the Paid checkbox on each entry.
  4. Next, select Credit Card for the Payment Method. If you select Debit, the transaction will not be processed by Worldpay from the FIS iQ portal.
  5. This will trigger the Collect Payments button to appear. Click this button. Don’t worry about filling in the Credit Type and Auth/Check #, these will fill in automatically when the card is swiped.
  6. If the patient has a card saved on file and they would like to use a different card for this transaction, you’ll need to click Use Another Card.
  7. If the patient does not have a card on file or has opted to use a different card, you’ll receive a Waiting for input message. At this point, it's always good to ensure that the Transaction Amount aligns with the total charges.
  8. If the card is present at the time of the transaction (and not on file), swipe the card. If successful, you’ll see the following message and credit card details. If the patient decides they want to use another card, click Change Card and swipe the new card.
  9. If the card is not present at the time of the transaction (and not on file), you’ll need to get the card information from the patient. The level of detail required is dependent on the configuration of the device. If you have chosen to go with our suggested Configuration #4, you’ll need to ask for the Card Number, Expiration Date, Security Code, and Billing Zip Code. The device will prompt you for each required piece of information. If you enter the card number incorrectly, the device screen will show an Invalid error. Use the Cancel button and start again.
  10. Once you’ve finished entering in the details press the Enter key. You’ll see the following message and credit card details. If the patient decides they want to use another card, click Change Card, and key in the new card details.
  11. This is your last opportunity to verify the transaction amount before processing the card. The Amount indicated in the Transaction Information section will be charged to the card. Once you’ve confirmed the transaction amount, click Process Transaction. Alternatively, if you need to make edits, click the Cancel Transaction link.
  12. You’ll receive confirmation that the transaction has been processed. If the transaction was denied, you’ll need to restart the process and run a different card. If this card is not currently saved on file, the Save Card button will appear.
  13. The system will display a confirmation once saved.
  14. Once the transaction has been processed and approved, select one of the following actions and click the Play button.

Save Card on File

Is saving a card on file secure?

When you elect to save a card on file, Worldpay creates a unique token that is saved within our system along with the last 4 digits of the card number (for identification purposes). The account information associated with the card is only stored with Worldpay. When a transaction is processed using a saved card, we send the token to the Worldpay system which then accesses the account details.

How many cards can I save on file?

You have the option to save up to two cards per patient. When you collect a payment, a warning will display if you’ve reached the maximum number of saved cards for that patient. At this point, a card will need to be deleted in order to save a new card.

Can I store a debit card?

Yes. In order to store a debit card, it must be processed using  Credit Card as the Payment Method and be branded by a major credit card (i.e. Visa), and the patient must not have reached the two-card maximum. The card reader and system are unable to accept or store debit PINs.

Can I store HSA/FSA Cards?

After you process an HSA/FSA card using the FSA Card method, the option to save the card on file will be present if the patient has not already reached the two-card maximum.

How do I delete a saved card?

When processing a patient payment, select the trash can icon next to the payment method you’d like to delete.

HSA/FSA Payments

You can process payments using an HSA or FSA card following the same process described above. The only recommended difference is selecting HSA Card as the  Payment Method. This will help you better understand your card type mix in reporting. Occasionally, you may need to process a partial payment if the patient’s account cannot cover the full appointment amount.

Reporting: Payment Log

When running the Payment log, you’ll be able to sort by HSA Card as a payment method, allowing more detailed reporting on your transactions.