Step-by-Step EHR Integration Process Guide for Custom EHR Integration

If you’re reading this in 2025, then do you know the amount of data that is being generated annually by the healthcare industry?

The compound annual growth rate of healthcare data is estimated to be 36%, which is actually the most with respect to every industry out there, huge right!

To give you an idea about its volume, it’s almost 6% faster than the manufacturing sector, 10% faster than financial services, and 11% faster than the media and entertainment. With this compound annual growth of data for healthcare, many processes can be streamlined and mined to gain valuable insights.

This is also one of the major reasons why many healthcare practices are looking to integrate the base of healthcare data into their practice’s custom healthcare software systems. This unique requirement of healthcare practices has increased the demand for EHR integration services and brought healthcare integration and interoperability back into the limelight.

But oftentimes, there are complaints about the expensive nature of custom EHR integration, right?

Technically, explaining EHR integration would be very simple, but its practical applications would be hard to imagine at first glance. To make it simple, let’s try to understand the EHR integration process and explain why it’s a little more expensive. Though by partnering with the right partner, as Thinkitive, you can find a way to save something on the EHR integration services, but that’s a blog for different times.

On that note, let this blog not only act as an EHR integration process guide for you before making a final decision about hiring custom EHR integration services from healthcare IT vendors.

So, without further ado, let’s get started!

Step 1: Assessment & Planning: Laying the Foundation

Planning is the most essential part of any integration. You see, the only fault in Alan Turing’s Christoper was that missing link between the encrypted messages, right? After all, what you need to find in another system makes the search much easier.

And since we’re talking about the bridge that we’re building, the bridge systems—ehr integration—let’s have a look at what you need to do before actually doing, and that actually makes up the first part of your EHR integration process.

• Current State Evaluation

Something that you wouldn’t change in this scenario is the systems. So, begin by analyzing your current software system. By evaluating the system inventory and connectivity assessment, you would know how your data is being stored, carried out, and managed by your system. Along with that, you would also know how the data flows into your system.

By knowing the data flow, you can identify the data flow mappings across the existing system, sorting and simplifying the further processes of data mapping. When doing this, document the things that you want to improve in the data flow or presentations. In simple terms, understand the pain points and also the opportunities that can be helpful for you in the EHR system integration.

• Requirements Definition

While assessing your system for electronic medical records integration, there are bound to be certain shortcomings. These might come in the form of data mapping or checkpoints, APIs, etc. Due to these shortcomings, the system will probably not be able to locate the exact data that you’re looking for.

These assessments will help you identify these shortcomings, and all you need to do is address them in the EHR integration process. Simple!

Well, not exactly, and there’s a business case for that as well.

• Business Case Development

Let’s say that you’ve done your research, noted the gaps, and are just waiting for the approval to go ahead. But before making this decision, you need to make sure that this EMR system integration will help you both clinically and financially for your practice.

One of the best ways to do that is by calculating the ROI of this entire EHR integration process venture. If it gives you a clear advantage in the short or long run, then and only then, you need to plan and budget your finances accordingly. 

Once that is done, map out the timelines and development milestones so that everything is smooth, etc.

Note: I know reading and applying this can be a little tricky. But worry not, this simplified version of the EHR integration requirement gathering can give you a heads-up in the process.

Step 2: Architecture Design & Technical Approach

Addressing the shortcomings of your practice’s healthcare system will lay the foundation for the integration of electronic medical records. Now, it’s time to build the structure or design the digital landscape that supports your EHR system integration.

• Integration Architecture Patterns

Let’s begin with the integration architecture patterns. Given your relevance and expertise in the healthcare industry, you would probably need a point-to-point integration model or hub-and-spoke integration model. While there is a significant difference between these two, knowing these will smoothen the next phases.

In point-to-point electronic medical records integration, you directly connect your system with the system with which you want to communicate or share information. Though this EHR system integration model can be simple and fast to implement, it can be complex with the number of systems involved and also the number of connections you want to establish.

On the other hand, with hub-and-spoke EHR system integration, you basically create a central hub for all the connections between the systems. This means that instead of communicating or connecting directly with the system endpoints, every point first connects with the central hub and then goes to the other system to fetch, receive, or update data. Despite the hub acting as a single point of failure, it can greatly simplify data architecture, security, and maintenance of connection and is highly recommended for complex systems.

• Service-Oriented Architecture

After finalizing the integration model, the next step is to choose the healthcare IT architecture that supports your integration and gives you additional benefits that just support you as well. For instance, with a service-oriented architecture, you get to harness the specific features of your EHR system. It will not only streamline communication with standardized protocols but also offer scalability in the architecture and reusability of the components that are already built; you can release the EHR integration models sooner, it gives you agility in adopting newer technologies, and it’s easier to maintain these single architectures than the whole systems.

• API-first Approaches for Modern Integration

Then comes the API-first approach, which prioritizes designing and developing of APIs before building the underlying application logic. Since they have become a standard practice and somewhere a foundational block of modern software components, adopting this methodology can bring seamless data sharing between disparate systems.

• Healthcare Standards Selection

Consider healthcare data standards as the language your system uses for sharing data. This is the only reason why inconsistent data standards cause so much trouble in EHR system integration. HL7 v2 and FHIR are some of the standard healthcare data standards that can help you streamline data exchange across systems. By adhering to these data standards, you eliminate almost all the problems that might arise when integrating the EHR system.

However, depending on your needs, these standards can vary where HL7 v2 would be more beneficial and, in some cases, the HL7 FHIR formats. Choose carefully and move ahead with the document exchange standards. Since you will be sharing documents from your system as well, adhering to the standard document exchange standards like C-CDA, etc., can streamline document sharing as well.

• Technology Stack Decision

For the EHR integration process, the technology stack plays a crucial role, and it is indeed important to understand this for the growth of your practice and the sustainability of your EHR system integration.

In your technology stack, the integration engine is something you simply cannot miss. While there is a wide range of options like Iguana, MuleSoftware, etc., your evaluation criteria should be purely based on the scalability of its providers, ease of use, support and update, and cost. If certain EHR integration services check all your boxes, then move ahead with the one for electronic medical records integration.

TIP: API Management Tips: Enforce OAuth2, rate limiting, and encryption for security. Along with that, provide self-service portals and SDKs, document everything, and have lifecycle management to automate versioning, deprecation, and backward compatibility.

With the selection of the technology stack, you have almost entered the phase of planning and other things. After this, you will have to set up the development and testing environment to move ahead and start coding the custom EHR integration bridge.

Step 3: Development & Configuration Process

Now that we’ve come to a point where you actually start coding to develop a custom EHR integration bridge, here are some of the few very important things for EHR system integration development and configurations.

• Interface Development Process

All the data exchanges that happen between your healthcare system and the EHR system are seen on the software interface. This is the first step of your EHR integration process, and here are a few things that you need to consider:

You can either design your own interface or choose from the standard pre-defined interfaces. One of the best ways to choose the interface is by scanning the pre-defined templates and documenting the shortcomings so that you can include them just in case you choose a custom interface.

Also, choose an iterative development method so that you can easily break down the development approach into smaller sections. This not only makes the development process much easier but also quickly achievable.

And during the entire development phase, ensure that the code you are writing can be reused and build component libraries so that it can be easily accessible.

• Data Mapping & Transformation

One of the major parts of your EHR integration process is mapping the data and transforming it into a format that should be understandable for the systems so that the data can be exchanged. To do this, adopting a field-level mapping process should be considered. This is because it connects a specific field from your system to the EHR system, which makes data sourcing and exchange much more accurate and faster.

Given that you’ll need this system to carry out your clinical and administrative approaches, you can choose the terminology mapping in your data mapping process. What it basically does is the process of translating concepts from one terminology or code system or format to another. 

And while you’re doing this terminology mapping, and if you’re using a custom method in this, then you can also set transformation rules so that the mapping is accurate and consistent.

• Configuration Management

For the presentation of data in an understandable manner, you need to configure or arrange the data in a particular form or pattern and, in simple terms, standardize it. Also, you’ll be using certain versions of the configurations. By implementing version control, you can easily transform the data into the format you want.

Along with that, you also need to ensure that the IT environment in which it is configured is not changed. This can be easily tracked by environment management, and the most important part is documenting everything, as it makes management easier.

NOTE: The development part of custom EHR integration is not only technical, but it also requires keen attention to detail. Though I tried to keep this simple and minimal, if you really want to know the intricacies of the development process in the EHR integration process, then click on the button below.

PS – Is this too technical for you? Well, if you’re already stuck with something too technical during implementation, then read this step-by-step EHR integration implementation guide.

Step 4: Testing & Validation Methodologies

If you’re working in the healthcare industry, then you must be familiar with the customized healthcare software system. If not, then any custom healthcare system is built to perform a certain task, right? It is the functionality of doing that task that makes things easier for us.

However, during the building stage, there are certain requirements and expectations that it must meet. In the case of EHR integration, you need to ensure that the system is properly integrated and shares data with accuracy, and that is where testing and validation methodologies kick in. Let’s explore that in brief below:

• Test Planning & Preparation

Just like the planning phase of your custom EHR integration or healthcare software development, testing the EHR system integration or healthcare API integrations also requires planning. You see, the testing must have a purpose, right?

So basically, in test planning, the scope, objectives, resources, and approach for testing are defined. This is to ensure that the EHR integration aligns with the business objectives of your practice.

The first part of planning involves test case development and the approach you take for developing. For instance, test cases are designed to verify that the software meets the requirements and behaves correctly under different circumstances. Though this makes up a major part of testing preparation, it somewhere sets the design for functional and non-functional requirements, error handling, and edge cases.

The next part of this is a test data creation strategy. In this, you create data on which the features, functionalities, and behavior of the software can be tested in a realistic scenario.

Last but not least, the test environment configuration, where the configuration should mirror or replicate the production environment, such as software versions, network settings, etc., to avoid discrepancies or invalidate test results.

• Testing Methodologies

Now, when you get engaged with the EHR integration process, there will be multiple components that you’ll have to test, verify, and give the green light to move ahead. However, since the EHR system integration is built on many components, there are certain testing methodologies that you need to adopt.

For instance, for individual components of the EHR system integration bridge, you can use unit testing to test one unique component. On the other hand, you can perform integration testing to test the connectivity between these systems.

During this entire testing affair, validate the entire workflow to ensure that no stone is left unturned. Along with that, performance and load testing should also be conducted to ensure that the system is reliable under a heavy load of data and that the EMR system integration performance is not affected by external or internal factors.

• Validation & Certification

Adhering to regulatory standards or interoperability standards is a huge part of your EHR integration process. Regulatory adherence gives your system credibility and authenticity. Moreover, validation gives you an assurance that the systems, processes, and integration bridge consistently deliver the desired results, which are predetermined by the specifications and integration quality standards.

While you’re at it, also conduct conformance testing for your EHR system integration. It is nothing but a testing activity where a process or, in this case, data sharing between systems complies with the requirements of the regulatory bodies such as HIPAA, GDPR, local laws, technical standards, contracts, etc.

Once you conduct this, you enter the last stage of testing, which is user acceptance testing. This testing is conducted to check whether the end-users are able to use the software system properly, efficiently, and effectively.

Know about the reliable testing strategies for your EHR integration project, and be assured of quality and easy testing processes.

Step 5: Implementation & Deployment

Once you’ve tested the EHR system integration with your healthcare software system, you are somewhere ready with the custom EHR integration, which can be deployed for use. However, this stage is just as important as the very first step of requirement gathering. As you’re doing the development and testing in a controlled environment, the real-life and real-time scenarios can cause some issues. Here are some considerations that you must consider:

• Deployment Strategy Development

The first step of the last stage of the custom EHR integration process is developing a deployment strategy. You see, when you want to deploy a system or, in this case, system integration, you need to plan carefully so that the bridge doesn’t fail. For instance, there are phased implementations and big-bang implementations, and you basically get a choice when it comes to deployment.

In a phased implementation, you gradually roll out certain components for use, and then roll out one component after another until the end. Meanwhile, in big-bang implementations, you simply roll out the integration bridge in one go. There are certain challenges and benefits to both, and considering them both is necessary.

Along with that, rollback planning and contingencies should also be considered when making changes in the system. It is basically a plan that outlines the steps to take to reverse a certain change that is being made in the system. This helps the system with great length in terms of minimizing disruption and downtime.

I almost missed it. Develop a communication plan so that your team will always be on top of this during the entire deployment process.

• Go-Live Process

The go-live phase or process is nothing but the official launch of the new system into production. Some of the key steps in this process include user acceptance and performance testing to ensure the readiness of your EHR system integration. However, to ensure that your EHR system integration is reliable and compatible during the go-live process, you need to plan and execute the EHR integration process as per it.

Set up a support structure during the transition so that any problem that arises during the go-live process can be easily addressed. Along with this, issue triage and prioritization should be set up so that when a problem arises, the problems can be categorized, prioritized, and resolved without disrupting the other processes.

• Early Stabilization Activities

A major part of the go-live part of your EMR system integration is early stabilization options to ensure that the system is reliable and users are satisfied after immediate deployment. For instance, a major part of this involves monitoring the EHR system integration bridge and tuning the performance of the integration to ensure that it is always top-notch.

Just in case an issue arises, you should have a plan ready to rapidly solve the issue, as the issue can disrupt the process, and in this conquest, you can lose the trust of your customers. Some of the things that can help you in this are automating issue detection with custom alerts, setting up systematic triage and prioritization processes, and, most importantly, maintaining clear documentation and communications.

And the last stage of deployment comes in the form of user feedback. You see, you may or may not use the EHR integration, but your practice will, and the people using the EHR system integration with healthcare API integrations will encounter problems that you might not know. That is why user feedback collection is important so that you can enhance the system and make it more user-friendly to actually make their work easier.

After this, you’ll read about ongoing maintenance and management, but implementation support for EHR systems is something that you should know. Click on the link in this section to read more about it.

Step 6: Ongoing Management & Optimization

If you’re still here, then hang on tight; you’re about to read the most important part of the EHR integration process. Honestly speaking, the EHR integration process ends with successful deployment. However, the technological and healthcare landscape is ever-evolving, and as a practice, you need to be all over the place. That is why ongoing management of the integration of the EHR system is necessary along with optimization.

• Operational Support Structure

Since your system will be transferring huge volumes of data, it can be hard for a person to monitor everything. So why not set up a system that can monitor and alert you whenever a problem arises? By setting up a monitoring and alerting system, you can streamline the monitoring process. And set up a team so that the issues can be addressed in real-time without causing many disruptions.

• Performance & Reliability Optimization

While operational monitoring and support are one thing, the performance of the EHR system integration bridge cannot be ignored. The same thing follows in this as well, where you have to identify the KPIs and monitoring goals so that you can monitor the performance of the integration and how it is impacting your practice.

At this stage, you need to curate capacity planning and scaling structure so that the performance can be measured and the problems or issues can be identified to solve or scale the software. 

• Continuous Improvement Process

Lastly, you have to set up a continuous improvement process for your EHR system integration so that it aligns with the latest trends, technologies, and developments in the healthcare IT landscape. You can get a post-implementation review where you can easily identify the gaps in your system. And that can be enhanced with prioritization so that the system does not fall short of something.

Also, update and upgrade management systems with changes in the system. Read more about the change management for EHR integration project as it can help you keep your services up and running at all the times..

Frequently Asked Questions