Medesk's Online Patient Payment Solution & Integrations

As a clinic owner, are you aware that a growing majority of patients prefer digital payment options, and that patients who experience payment issues are significantly less likely to return to the same healthcare provider? These patterns show that offering a seamless online payment experience is no longer a luxury. It is a necessity.

Payment processing is a key challenge in many healthcare practices, especially as the industry shifts towards more patient-centred care. If you have already faced late payments, time-consuming claim processing, a lack of prepayment options, and patient loss due to inconvenient payment methods, it means you are looking for a solution that automates patient billing and enhances patient care.

Medesk, a versatile practice management platform, simplifies the process of collecting payments through an integrated patient portal and seamless connections to Stripe, Xero, and Healthcode. The platform allows clinics to manage payments easily, ensure faster processing, and boost patient engagement.

In this guide, we'll show you how to make the most of Medesk's payment service, starting with the basics of the patient portal, followed by integrating Stripe for credit card payments and Healthcode for insurance claims. Ready to learn how Medesk can make your clinic's financial experience more successful? Let's dive in.

Connect Stripe Integration and Don't Worry about Unpaid Bills

Medesk is designed to optimise healthcare practice operations, and its online healthcare payment system is one of the key components.

Getting started is straightforward. Create an account on the official Medesk website and you'll have immediate access to a 7-day trial, during which you can receive payments, configure flexible payment options, and evaluate the platform.

Medesk integrates with Stripe to handle credit and debit card payments securely, including CSC verification. This provides secure payment processing utilising point-to-point encryption, operating in full compliance with PCI DSS standards. Stripe operates in over 135 countries and is a trusted global solution for healthcare providers.

For UK-based clinics, Stripe's standard card processing rate is 1.5% + 20p per transaction for UK cards, with rates varying for international cards. There are no setup fees or monthly charges when using Stripe through Medesk, and there are no hidden costs. The integration also supports digital wallets for clinics, including Apple Pay and Google Pay, giving patients the flexibility to pay using their preferred method on any device. Additionally, clinics can securely keep a card on file for recurring payments or outstanding balances.

The Medesk and Xero integration takes automated invoicing further by syncing every payment and invoice instantly to your accounting software, removing the need for manual reconciliation. When a patient pays through the portal, the transaction is recorded, the invoice is generated, and your Xero account is updated automatically. Clinics using automatic payment reminders and a streamlined checkout process consistently report fewer late payments and improved cash flow.

To activate the function, go to Settings → Payments and Accounting → Stripe:

Authorise your existing Stripe account or create a new one using the registration form. Once connected, the status changes to Connected. All payments made through the patient portal go through Stripe automatically, and every transaction appears in your Medesk dashboard so you can track paid and pending invoices at a glance.

Medesk's Patient Portal: Simplifying Online Payments for Your Clinic

One of the biggest advantages of Medesk is its patient portal, a secure and user-friendly platform where patients can handle online bill pay in healthcare from any device, without needing to contact the clinic directly. Implementing prepayment rules and giving patients easy access to their outstanding balances leads to more predictable revenue and fewer no-shows. Tools like The QR Code Generator (TQRCG) can also support seamless payment workflows by enabling clinics to share quick-scan payment links with patients.

Patients booking online can be asked to pay either in part or in full for your services before their appointment can be considered confirmed. You can easily define your prepayment rules by navigating to Settings → Online Booking → Prepay.

You can require a Minimum Prepayment for booking confirmation. Two types of prepayment are available: Fixed Value and Percentage of Total Cost. After configuring this, all patients will be redirected to a prepayment page at the end of the booking process. Even once Minimum Prepayment has been enabled, patients will still be able to pay the full amount for services booked if they want. For larger bills, patients can choose to pay a portion now and settle the remainder later, making it easier to manage their healthcare expenses over time.

Appointment bookings left without prepayment will be given the status "Pending prepayment". You can define a set time after which postponed prepayments can no longer be made and the associated booking will be cancelled automatically.

Medesk sends automatic text-to-pay requests and SMS payment reminders to patients about upcoming payments, reducing the risk of late or missed payments.

The same shift is visible outside healthcare: businesses in other service industries are launching branded digital wallets to give their customers faster, more flexible ways to pay, and those customers include your patients.

Links to the patient portal can be found in Settings → Online Booking. Publish it on your website, social media, and patient review aggregators to increase your reach to potential customers and accept contactless payments.

With the Medesk online payment module, you'll slash the likelihood of no-shows and cancellations and make it incredibly easy for patients to understand exactly what they are paying for.

"Implementing portal functionality helped us to optimise workload at the reception desk, reduce our phone bill, increase patient acquisition via our website, as well as become more available to our patients." a Prime Clinic case study.

Automate Insurance Claims Processing and Medical Billing

For clinics working with insurance claims, Medesk offers Healthcode integration. Healthcode is a platform used by healthcare professionals in the UK to handle private medical insurance claims efficiently. As an integrated patient billing platform, Medesk connects claim submission, invoice management, and financial reporting in a single workflow rather than requiring staff to switch between disconnected systems.

Here's how Healthcode integration benefits your clinic:

• Automated submissions reduce the risk of human error in claim details.
• Clinics can generate detailed reports on claim statuses, allowing for better financial oversight.

To integrate Healthcode, navigate to Settings → Healthcode, enter your login credentials, and select the insurance companies you work with.

Once connected, issuing an invoice in Medesk lets you verify the patient's insurance policy against Healthcode's records. If the policy is valid, you can prepare and send the invoice directly to the insurer through the integration. After submission, clinic staff can monitor each claim's progress directly within Medesk: accepted claims update automatically, while rejected or queried claims are flagged so your team can act without manually chasing the insurer. This visibility means billing staff spend less time on follow-up calls and more time resolving genuine issues. Creating invoices in Medesk is subject to strict regulation to ensure that you avoid making mistakes and to speed up the process of working with insurance companies.

Medical billing can be simple and straightforward when there is an insurance company involved, but less so when the patient is paying themselves. We have integrated the Medesk healthcare accounting software with Xero to offer you the utmost in convenient accounting and financial reporting.

To connect your Medesk account to Xero, go to Settings → Payments and Accounting → Xero and click Connect. Authorise the connection using your Xero credentials.

Once connected, automated invoicing takes over. Every invoice created in Medesk is synced to Xero automatically, and every recorded payment appears in your Xero account within minutes. Your accountant always has an up-to-date view of clinic finances without any manual data entry.

Whenever you create an invoice or record payments in Medesk, this information is synced to Xero for your accountant. All invoices can be created either from the patient record or from the calendar by selecting the desired appointment.

Then you can send the invoices via email or print them with a few clicks. This is how your documents will look with the Medesk platform:

The Medesk billing module helps you not only track and manage payment processes, generate invoices, and handle claims, but also do payroll calculations.

Security and Compliance in Healthcare Payments

Handling patient payments means handling sensitive personal and financial data. For UK clinics, that comes with clear legal and regulatory obligations. Any online patient payment solution you use must meet the standards set by both GDPR and PCI DSS, and Medesk is built with these requirements in mind.

GDPR governs how patient data, including payment records, is stored, processed, and shared. Medesk keeps patient financial data within secure, encrypted systems and does not share information with third parties beyond what is required to process the transaction.

PCI DSS (Payment Card Industry Data Security Standard) sets the technical requirements for any system that handles card payments. Because Medesk processes card transactions through Stripe, which is a certified PCI DSS Level 1 provider, clinics benefit from enterprise-grade card security without needing to manage compliance themselves.

In practical terms, this means:

• Card details are never stored on Medesk's servers. They are tokenised by Stripe at the point of entry.
• All data transmitted between patients, the portal, and the payment processor is encrypted using TLS.
• Access to financial records within Medesk is role-based, so only authorised staff can view or manage payment information.

For clinic owners evaluating online payment options, security and compliance should be non-negotiable criteria. A data breach or non-compliant payment process can result in significant fines under GDPR and damage patient trust in ways that are difficult to recover from. Choosing an integrated platform like Medesk removes the burden of managing these obligations across multiple disconnected systems.

Frequently Asked Questions

1. What are online payment solutions in healthcare?

Online payment solutions are digital portals integrated directly with your medical billing software to facilitate secure credit, debit, or insurance payments. They allow patients to easily settle their bills from any device without needing to visit the clinic or mail a check. This technology streamlines revenue cycle management for healthcare providers.

2. What does it cost to use Medesk's online payment system?

Medesk offers a permanent Free plan, available in every market, plus paid plans for additional features. Medesk does not charge additional transaction fees on top of your Stripe processing costs. For UK clinics, Stripe charges 1.5% + 20p per transaction for UK-issued cards. There are no setup fees or hidden charges, so your total cost per payment is predictable from day one.

3. How quickly do patient payments reach my clinic's bank account?

Through Stripe, payouts are typically processed within two business days of a completed transaction. Once your Stripe account is fully verified, you can also configure a custom payout schedule to match your practice's cash flow needs.

4. Can patients pay using Apple Pay or Google Pay?

Yes. Medesk's Stripe integration supports digital wallets for clinics, including Apple Pay and Google Pay. Patients can use these methods directly through the patient portal on any compatible device, without needing to enter card details manually. Reliable payment processing also helps clinics maintain a stronger business credit score by improving cash flow and reducing missed payments.

5. Does Medesk support pay-by-link or Open Banking payments?

Medesk's patient portal generates a personalised payment link that can be shared via email, SMS, or published on your website. This functions as a pay-by-link solution, allowing patients to settle invoices remotely without visiting the clinic. Medesk continues to expand its payment method support in line with evolving UK payment standards.

6. Is Medesk compliant with GDPR and PCI DSS?

Yes. Medesk processes card payments through Stripe, a PCI DSS Level 1 certified provider, and the platform is built in compliance with GDPR requirements for healthcare data. Patient card details are never stored directly on Medesk's servers.

7. What happens if a patient does not complete their prepayment?

Bookings left without prepayment are given a "Pending prepayment" status. You can set a time limit after which the booking is automatically cancelled if payment is not received, helping you protect your schedule and reduce no-shows.

8. How can patients pay a medical bill in instalments or partial amounts?

Medesk's prepayment configuration supports both fixed-value and percentage-based minimum payments, meaning patients can pay a portion of their bill at the time of booking and settle the remainder later. Clinics set the minimum amount required for booking confirmation, so patients always know upfront what is due now and what can be paid at or after their appointment. This flexibility makes it easier for patients to manage larger healthcare expenses without having to contact the clinic to arrange a payment plan manually.

9. Can patients pay their medical bills online through Medesk?

Yes. Medesk's patient portal gives patients a secure, web-based space where they can view upcoming appointments, see outstanding balances, and complete payment using a credit or debit card via Stripe. The portal is accessible from any device, so patients can settle bills at any time that suits them, without calling the clinic or attending in person.

Take Control Over Your Revenue Cycle Today With Medesk's Free Trial

Whether you're handling patient payments through credit cards, insurance claims, or both, Medesk offers a solution that reduces the administrative burden, speeds up payment processing, and improves the patient experience. By integrating with Stripe, Xero, and Healthcode, Medesk lets you manage all payment needs from a single platform.

Our client, Clinic Aesthetic, says that the possibility of online payment and online consultations has led to the clinic attracting patients from other parts of the country and even abroad. Read other reviews and case studies on our website and Software Advice page.

Medesk has a permanently free plan for up to 2 users, 1,000 patient records, and 50 appointments per month, with no credit card required. The Pro plan adds unlimited users and unlimited patient records, with a 7-day free trial. For full details, see our Pricing page.