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Understanding Payment Processing Fees and How They Impact Your Bottom Line

Understanding Payment Processing Fees and How They Impact Your Bottom Line


Payment processing might not be the most exciting part of running a hospital—but it’s one of the most important. And while it may seem straightforward, every swipe, tap, or click comes with a cost.

It’s tempting to focus only on finding the lowest possible rate. But here’s the bigger picture: 

❓ What are you really getting for those fees?

⏱️ How much time is your team spending on reconciliation, refunds, or fixing billing mistakes?

📉 And what could it mean for your bottom line if those tasks were faster, easier, and less prone to error?

Let’s break it down.

💰 Where Processing Fees Go (and What You’re Paying For)

When a pet owner pays with a card, several players take a small cut:

  • 🏦 The cardholder’s bank (like Chase or Bank of America)
  • 💳 The card brand (like Visa or Amex)
  • 🧩 The payment processor (the technology powering the transaction)

Each one takes a percentage from the total. On average, veterinary hospitals see around 2.4% in total fees per transaction. The majority of that—about 1.9%—goes to the cardholder's bank. A smaller portion (roughly 0.14%) goes to the card brand, and the rest—typically 0.1% to 0.4%—goes to the payment processor.

That’s why it’s so important to know what you're getting in return for the piece your processor takes.

Sometimes, the lowest rate doesn’t give you the most value. So instead of asking How much does it cost? it’s worth asking: What am I actually getting for that fee?

🚨 Hidden Inefficiencies: The Costs You Don’t See on the Invoice

If your payment system isn’t fully integrated with your EMR, you’re likely paying in other ways:

  • Manual reconciliation between systems at the end of the day (hello, cold Taco Bell at the computer)
  • Delayed or failed refunds that frustrate clients and staff
  • Disputes and chargebacks that your team has to navigate solo
  • Fragmented reports that make it hard to track down payment issues

The result? More staff time wasted, more errors, and more stress.

🛠️ A Better Option: Integrated Payments Built for Veterinary Hospitals

That’s why we built a modern, fully integrated payments experience in Instinct EMR—designed specifically for the fast pace and complexity of veterinary hospitals.

With our system:

  • Refunds take just 4 clicks—and neither the client nor their card needs to be present.
  • Dashboards and payment records sync in real time.
  • Chargeback disputes? We’ll handle them for you (and help prevent them in the future).
  • Customize your batch close time to match your hospital’s actual business day.
  • 🚫  No hidden fees. No surprise rate hikes. Ever.

And with tools like Link to Pay and mobile-ready, terminals (now with a longer idle timeout), it’s easier than ever to meet pet owners where they are—at the front desk or on the go. 

👩‍⚕️ More Than Just a Front Desk Tool

We hear it all the time: “Our doctors don’t deal with payments.”

Totally fair. But here’s where it does affect them:

  • When they’re waiting on a payment to start care
  • When limited payment options delay treatment decisions
  • When support staff are stressed from navigating preventable friction

Integrated payments help reduce those bottlenecks. That means fewer delays, smoother communication, and more time focused on patient care. 

⏱️ Efficiency You Can Measure

Here’s a stat that might surprise you: For every 100 transactions, hospitals using Instinct Payments save about 7 hours of staff time.

That’s time your team could use to:

👩‍⚕️ Take on another case

📞 Return a call from a worried pet owner

🥗 Actually eat lunch

Small moments add up. And so do the dollars. 

🧡 You Deserve Better Than ‘Good Enough’

Payment processing doesn’t have to be a black box. And it definitely shouldn’t be a burden. With the right system, it can be a quiet hero of hospital efficiency, saving time, reducing errors, and giving your clients a smoother experience.

That’s why we built Instinct Payments as a core part of Instinct EMR—not just to check a box, but to support the same goals your team works toward every day: clear communication, seamless workflows, and exceptional patient care. 

Because great practice management software doesn’t hold your team back. It grows with you, evolves with your hospital, and makes the hard things just a little easier.

If you’re already using Instinct EMR, we can help you activate integrated payments so you can start seeing the benefits right away. Reach out to your customer support manager to get started with Instinct Payments. 

And if you’re not using Instinct EMR yet? We’d love to show you what’s possible. Schedule some time with our team, and let’s make every swipe count.