ERP Data Migration Best Practices for Health Systems

What is ERP data migration in healthcare?

Unique challenges in healthcare ERP data migrations

Healthcare environments introduce multiple challenges when migrating ERP data:

• Strict audit requirements: IRS, HIPAA, and OSHA regulations mean healthcare data migration must be auditable and secure.
• Data security risks: Older ERP systems are vulnerable to cybersecurity threats, especially when no longer supported by vendors.
• High volume of structured data: Employee records, pay history, and benefits data must remain accessible and compliant for 7 years or longer.
• Multiple overlapping systems: HR, supply chain, and finance platforms may all be legacy ERPs, each with different data formats and deprecation timelines.

As highlighted in ERP Data Archiving for Healthcare, retaining data in legacy ERP systems without a secure archive leads to compounding legal, financial, and operational risks.

ERP data migration best practices for health systems

The following best practices help mitigate risk and create long-term value:

Develop an ERP data migration plan that starts with system inventory

A clearly defined ERP migration plan sets the scope, timeline, and responsibilities for the ERP data initiative. It prevents confusion about what should be migrated versus archived and ensures alignment across IT, HR, finance, and compliance teams, making it essential for controlling costs and avoiding delays or redundant work.

This migration plan should start with an internal inventory of legacy ERP systems. Document the types of data housed in each system (HR, payroll, finance, etc.), who uses it, and for what purpose. This inventory informs critical decisions throughout the ERP data migration process and should be developed in collaboration with a vendor that understands healthcare-specific data categories and retention requirements.

Define what to migrate vs. archive

Not all ERP data belongs in the new environment. In fact, migrating every legacy data set can inflate costs, complicate system usability, and introduce unnecessary risk. A well-structured ERP data migration should define which records require active access and which can be safely archived in a secure, searchable repository.

Align stakeholders from IT, finance, HR, and compliance to identify access requirements and retention mandates. For example, current employee payroll data may need to be migrated for ongoing processing, while records from terminated employees can typically be archived, provided they remain accessible for audit or legal requests.

Consider factors like system usage patterns, reporting needs, legal hold status, and state-specific retention laws. Categorizing data upfront allows HIT departments to reduce data volume, streamline migration workflows, and accelerate ERP decommissioning timelines.

For guidance, refer to the categories of ERP data and their migration requirements, a practical framework for distinguishing which datasets need to move forward with the new system and which can remain secure in an archival platform like DataArk.

Align with retention schedules and audit needs

One of the most overlooked risks in healthcare data migration ERP projects is the failure to align data handling with legal retention mandates. Federal and state laws may require ERP data to be retained for 7 years or more, depending on the type, particularly payroll, HR, and financial records. If this data is purged too soon or housed in non-compliant environments, the legal and operational consequences can be severe.

To prevent exposure, healthcare CIOs should work closely with legal, compliance, and records management teams to map each data category to its required retention period. Archived data must remain accessible for audits, internal reviews, or legal inquiries, even long after the original ERP has been retired. Using a HITRUST-certified ERP data archiving platform like MediQuant’s DataArk ensures the archival system enforces retention rules and safeguards protected data, while freeing healthcare teams from the burden of managing legacy infrastructure.

Validate usability and access

Beyond solely focusing on moving data, ERP data migrations must also preserve its usability. Healthcare organizations often assume that once data is archived, it will be easy to retrieve. But unless the ERP data archiving solution includes role-based access controls, searchable fields, and full audit trails, HIT teams may struggle to locate what they need when they need it.

CIOs should prioritize validation testing to ensure that migrated and archived datasets remain accessible across departments like HR, finance, and legal. This means confirming that users can generate required reports, respond to audits quickly, and retrieve records without IT intervention. Modern healthcare data migration strategies should also verify that systems provide complete chain-of-custody tracking and maintain metadata for defensibility.

If archived ERP data is difficult to navigate, it will undermine operational continuity and increase the risk of compliance violations, defeating the purpose of the migration in the first place.

Prepare to sunset the legacy systems

A truly successful ERP data migration enables full decommissioning of legacy systems. After validating that archived data remains accessible and usable for all necessary stakeholders, CIOs should confirm that every critical use case across HR, finance, compliance, and legal is fully supported in the new environment or archive.

Once that validation is complete, it’s time to shut down the original system. Fully sunsetting legacy ERP platforms is what allows health systems to unlock the true ROI: eliminating licensing fees, reducing infrastructure and support costs, and reducing risk exposure from outdated or unpatched systems. For a deeper look at the financial and operational upside, see The ROI of Archiving Legacy ERP Data.

This is also a critical moment for CIOs to take a structured, board-ready approach to system retirement. MediQuant outlines this process step-by-step in ERP Decommissioning Strategy: A CIO’s Step-by-Step Guide, which includes how to align stakeholders, validate system access, and retire platforms with confidence.

Equip stakeholders for a smooth ERP data transition

The success of any ERP data migration project depends on how well internal teams are aligned, informed, and engaged throughout the process.

The first step for CIOs to take is to establish clear ownership to avoid bottlenecks and align expectations. Assign leads from each department to define data requirements, approve access controls, and validate post-migration usability.

A key enabler of success is structured communication. Set up a cadence of cross-departmental check-ins with a central project manager overseeing progress and risks. Ensure each team understands what data they will retain access to, how they can retrieve it post-migration or in an archive, and what changes to expect in their workflows.

Don’t underestimate the value of documentation and training. Many ERP data migrations fail to fully decommission legacy systems because teams feel unsure about how to access the historical data they need. Providing training, FAQs, and archived report templates helps teams feel confident in the new setup and reduces reliance on IT for routine access.

Finally, engage internal stakeholders early in vendor selection. The right vendor should understand the functional needs of each department as well as proving deep expertise in the specific ERP systems the organization is moving to and from. A vendor like MediQuant, with industry-leading expertise, can help facilitate these conversations and guide teams through the process with a focus on usability, compliance, and long-term value.