Expert guide to data migration in healthcare

Key takeaways

  • Data migration in healthcare comes up when the business is forced to shift from an unsupported software version or wants to switch data warehouses, change EHR or CRM vendors, expand the storage capacity, enable data interoperability, or strengthen compliance.
  • Before the migration, you need to consider legacy infrastructure, data requirements, input sources, tag management, cost management, downtimes, and tech compatibility.
  • Core medical data migration steps are data assessment, extraction, cleaning, transformation, loading, testing, verification, and reconciliation.
  • After the migration, you should take time for optimization, change management, data synchronization, mapping, security, quality, legacy system decommissioning, workflow improvement, and training.

If you’re at the point where you’re considering a migration, chances are you’ve already run into issues with outdated systems, fragmented records, or inconsistent data. Sound familiar?

You’re smart not to put off healthcare data migration. The pressure to keep patient information consistent, accessible, and interoperable is intense. Yet the latest data shows that while 70% of US non-federal acute care hospitals can exchange PHI, only 43% do it routinely. That gap between capability and consistent execution often comes down to one thing: how well the underlying data is stored, structured, and how accessible it is.

The benefits of proper healthcare data migration go far beyond just moving files. From what I’ve seen, when done well, a migration pays off in faster data access, higher performance, better interoperability, cleaner data, and lower administrative burden. Done poorly, it hinders care workflows. My team and I have been working on dozens of complex data migration projects and have dealt with just about every compatibility quirk you can imagine.

That’s why in this article, I’ll walk you through exactly how to do a data migration in healthcare — the right way.

When medical data migration is required

The talks of healthcare data migration usually come up when the pain of staying with your current setup outweighs the disruption of moving. It’s triggered by these common scenarios:

  • Switching data warehouses when the old one can’t keep up with the volume of data.
  • Changing EHR or CRM vendors because the current platform no longer fits workflows, lacks integration options, or modern features. 
  • Migrating to cloud-based infrastructure to rely less on expensive on-premise servers, scale and access data more easily.
  • Increasing storage needs as imaging data, lab results, and historical records pile up faster than expected.
  • Ensuring data interoperability so that data flows seamlessly across systems and teams.
  • Meeting regulatory requirements for data handling, which often demand high levels of encryption, access control, or auditability.

What worries me most is how long many organizations wait before tackling the inevitable. According to KLAS research, 42% of small independent hospitals are still running on legacy systems. Migrating data from them to newer software would be smarter, because legacy systems tend to be brittle, vulnerable, and resistant to integration.

I push clients to view migration from legacy apps not as a cost but as a safeguard. Every year, healthcare relies on data more and more. Just look at the trends shaping healthcare in 2026 and beyond: preventative care, artificial intelligence, and analytics-powered precision medicine. They are only as strong as the data infrastructure that supports them.

Types of healthcare data for migration

You’ve definitely worked with all of these healthcare data types and know them from experience. But for the sake of clarity, let’s break them down into 4 categories. I’ve touched more upon this topic in another article, and you’re welcome to check it out. 

  • Clinical data. It includes electronic health records, demographic data, medical images, clinical trial data, health history, lab tests, etc. 
  • Administrative data. This category covers things like workflow data, staffing schedules, appointment lists, healthcare asset data, and others. 
  • Patient-generated data. Within this one, we group everything from vital signs and patient symptoms to activity tracking and lifestyle information.
  • Financial data. Here goes operating expenses, treatment costs, billing records, insurance coverage details, and reimbursement data.

Trust your healthcare data to migration experts

6 pre-migration considerations for healthcare data

Talking from experience, the projects that succeed are the ones where preparation is as serious as the migration itself. If you lay the groundwork properly, you avoid the kind of chaos that can influence the daily work of healthcare professionals.

So, how is data migration planning done? Here are 6 things you need to consider.

The legacy infrastructure & data requirements

Legacy systems often store data in proprietary structures, and they may trap you if ignored. Innowise’s experts take the time to map out data fields, dependencies, and compliance requirements so we are prepared for any challenges ahead.

Data input sources

Every hospital system has dozens of data input sources, like EHRs, imaging systems, lab software, and patient apps. Each input has to be accounted for and validated to ensure nothing gets lost or duplicated in transit.

Tag management

Healthcare files are rich in metadata — diagnosis codes, timestamps, physician IDs — and all of it must remain intact. If tags are lost or corrupted, critical context disappears, making records incomplete or even unusable. Strong tag management protocols prevent mislabeling that can derail accuracy.

Cost management

Budget not just for the technical work, but also for staff training, overtime, and contingency plans if things take longer than expected. Skipping this often leads to half-finished migrations, strained budgets, and unsafe shortcuts.

Downtime

Some interruptions are inevitable during migration, but the key is planning these windows carefully. Say, schedule downtimes for late nights, weekends, or opt for phased rollouts to minimize interruptions. And yes, clear communication with staff helps avoid panic.

Technical compatibility

Differences in database structures, data formats, and platforms between the old and new systems can create serious roadblocks. You need to identify these incompatibilities and plan for them. Otherwise, the migration risks turning into a series of costly workarounds.

EMR data migration is probably the most requested type of data migration I see. And for good reason. Healthcare organizations can’t afford data silos or inaccuracies. The EMR data migration best practices are boring but effective: meticulous data preparation, mapping, validation, and lots of test runs.

Portfolio Manager in Healthcare and Medical Technologies

Steps for migrating medical data

Assessment of prior data

My team and I always begin with a full data assessment: EHR records, imaging files, lab results, billing data, etc. We map out data locations, structure, and formats. More often than not, this reveals duplicates, gaps, or compliance risks that would cause problems if we tried to migrate blindly. Based on the assessment, we also select data migration methodologies.

Data extraction & cleaning

Once we know the healthcare data landscape, we pull the information out of the legacy systems in a structured way. At this point, we also clean the data: strip out duplicates, correct obvious errors, and flag incomplete records.

Data transformation

Raw data seldom drops neatly into the new environment. We normalize formats, standardize medical codes (e.g., ICD, SNOMED, LOINC), and align the data fields. Without this transformation, medical records are almost impossible to use in practice.

Data loading

When everything’s ready, we migrate the healthcare data. Depending on the client’s preferences, we either run a migration in one go or split it into phases. Usually, I recommend starting with non-critical modules. The important part here is having a controlled plan so nothing slips through unnoticed.

Data testing & verification

If the data is in the new system, it’s not the right time to relax. Here, my team runs checks to make sure records are complete, accurate, and accessible across modules.

Data reconciliation

Here, we compare old and new systems. Automated checks help confirm volume and consistency, while manual spot reviews ensure critical patient data hasn’t been altered or lost.

Post-migration considerations

Once the data is moved, it feels like you’ve crossed the finish line. But really, you’re only about 80% there. What happens afterward — optimizing, validating, training staff — is critical. Skip it, and you’ll just swap out the old headaches for shiny new ones.

Post-migration optimization

After go-live, we get into the weeds: tuning performance, adjusting indexes, tightening up integrations. The system that looked fine on paper has to handle real people, real workloads. A few smart tweaks here often mean the difference between “it works” and “this is actually fast and usable.” We also listen closely to clinicians: what’s slowing them down and what could be smoother. And then feed that back into improvements.

Change management

New workflows don’t stick if people don’t understand why they’re happening. That’s why we spend time on prep, training, and making sure leadership isn’t just signing off but backing the change. And yes, change fatigue is a real thing, so clear communication and staged rollouts usually keep it manageable.

Data synchronization

In phased migrations, when old and new systems run side by side, things can get messy fast. If data isn’t kept in sync, updates like lab results or patient admissions can fall through the cracks. That’s when staff start asking: “Which system is the source of truth?” We make sure they never have to wonder.

Data validation

Once the switch is made, we test if everything’s right. That means running real scenarios: pulling patient histories, checking reports, opening imaging files. If it works in practice, then we know the system is safe for everyday use.

Data mapping

Even with all the prep in the world, you still need reconciliation after the move. We double-check the mapping, compare old vs. new datasets, and confirm every field landed where it should. My colleague wrote a whole piece on data mapping in healthcare, and honestly, it’s worth a read if you want to understand why this step is so critical.

Data security & compliance

Every migration has to respect local regulations, like HIPAA, GDPR, FDA, MDR, IVDR, EHDS, BDSG, and CNIL. We check access controls, audit logs, and encryption, and make sure they’re working as intended.

Data quality

We add quality checks for duplicates, inconsistencies, and outdated entries. Over time, this stops the new system from drifting back into the same unreliable mess the old one became.

Legacy system decommissioning

The temptation is to keep old systems around “just in case.” But hanging on to legacy healthcare data platforms usually adds cost and risk without much benefit. Once the new setup is proven stable, we retire the old. It’s cleaner and safer that way.

Workflow optimization

Once hospitals are freed from the constraints of outdated tools, we often see better ways to admit patients, share imaging, and process billing. Those workflow wins can unlock ROI nobody was expecting at the start.

Training

And finally: migration isn’t done until training is done. Clinicians, admins, IT staff — they all need confidence with the new system. Quick guides, hands-on sessions, and ongoing support help turn “go-live” into a smooth process.

Ready to start migrating your healthcare data?

How Innowise ensures smooth migration of healthcare data

I’ve been around enough hospital migrations to know one thing: it’s never just about shoving data from one system to another. If all we cared about was “copy–paste,” sure, the job would be easy. But in reality, what matters is making sure doctors can keep treating patients while all that data is moving around.

That’s why, at Innowise, we don’t treat migrations like a box-ticking IT project. We truly dig in — auditing, cleaning, transforming, loading, reconciling. That’s the level of care I’d want for my own records. And honestly, the tech side is only half of it. Hospitals need help rolling with the changes: staff training, tweaking workflows, and making sure the new system works day to day. 

So what does “smooth migration” really mean? To me, it’s not just about avoiding downtime. It’s about giving providers a sturdier digital foundation for what’s next in healthcare. That’s the bar my team holds itself to. If you want a fuller breakdown, we’ve laid it all out on our healthcare data migration services page.

Aleh Yafimau

Senior Technical Delivery Manager in Healthcare and MedTech

Aleh has a strong grasp of what makes healthcare and MedTech software truly work. He leads with both technical clarity and sector knowledge, making sure every project delivers long-term value — not just code that runs, but systems that matter.

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