Integrating Dynamics 365 with EHR Systems: A Step-by-Step Guide

If you’re a healthcare company looking to connect patient records with your CRM, this guide is for you.

Microsoft Dynamics 365 is a powerful tool. But when it’s connected to your Electronic Health Record (EHR) system, it becomes even more valuable. Why? Because your teams can work faster, smarter, and with better data.

Let’s walk through how to integrate an EHR with Dynamics 365.

Why integrate EHR with Dynamics 365?

Most EHRs are great for clinical work, but not built for patient engagement or outreach. Dynamics 365 fills that gap. Together, they allow you to:

Keep patient data in sync across platforms

Track communication and appointments in one place

Automate follow-ups and care plans

Get a 360-degree view of the patient journey

What you’ll need

Before starting, make sure you have:

Access to Microsoft Dynamics 365 (typically Customer Service or Sales module)

Access to your EHR system (e.g., Epic, Cerner, Meditech, or a custom-built one)

A middleware or integration layer — like FHIR API, Azure Logic Apps, or Power Automate

API access credentials for both systems

Developer or IT team support (some steps are technical)

Step-by-step integration process

Step 1: Understand the EHR's API capabilities

Most modern EHRs support FHIR (Fast Healthcare Interoperability Resources) — an industry standard for exchanging healthcare data.

• Confirm that your EHR exposes FHIR APIs
• Identify endpoints like Patient, Encounter, Observation, etc.

Set up a secure API connection

You’ll need:

• OAuth 2.0 authentication (EHRs usually require secure token-based access)
• App registration in Azure AD if you're using Microsoft services
• Define scopes and permissions for your app (e.g., read/write access to patient data)

Step 3: Use Azure Logic Apps or Power Automate

These tools help bridge Dynamics 365 and the EHR system without needing heavy custom code.

• Choose a template (or start from scratch)
• Use HTTP connectors to call the EHR API
• Use Dynamics 365 connectors to create/update records like Contacts, Cases, or Appointments

Example: When a new patient is added to your EHR, automatically create a new contact in Dynamics 365.

Step 4: Map your data fields

Align the data between both systems. Common mappings include:

EHR Field Dynamics 365 Field
Patient.Name Contact.Full Name
Patient.DOB Contact.Birthdate
Patient.Email Contact.Email Address
Appointment.Date Appointment.Scheduled Date

Make sure data types match and account for optional fields.

Step 5: Test and validate

Start with a test environment. Run a few use cases, such as:

• Sync a new patient record
• Update a diagnosis or case note
• Schedule an appointment and verify in both systems

Check for data delays, formatting issues, or permission errors.

Bonus: Keep it secure

• Use encryption for data in transit
• Apply role-based access in Dynamics 365
• Audit all API activity and log events
• Regularly review and update permissions

Final thoughts

EHR and Dynamics 365 don’t have to live in silos. By connecting them, your teams can improve patient communication, reduce manual work, and deliver better care.

At 3iX Consulting, we help healthcare providers design and implement these integrations — securely and efficiently.

Need help connecting your EHR to Dynamics 365?
Let’s talk → 3iX Consulting