2025 CMS Final Rule Update: EHRs Must Be a Qualified Registry to Submit Quality Data and What It Means for Healthcare Organizations
- Miranda Stork M.B.A.
- May 14
- 3 min read
Updated: May 21
In a significant shift for the healthcare technology landscape, the Centers for Medicare & Medicaid Services (CMS) finalized a rule that will impact how Electronic Health Record (EHR) systems can submit quality data. Under the 2025 CMS Final Rule, EHR vendors can no longer directly submit data to CMS unless they are formally recognized as a Qualified Registry (QR).
This change reflects CMS’s broader efforts to improve data quality, accountability, and transparency in the Quality Payment Program (QPP) — and it will have wide-reaching implications for providers, EHR vendors, and healthcare organizations alike.
What Changed with the 2025 CMS Final Rule?
In previous years, EHR vendors could submit clinical quality measures (CQMs) or electronic clinical quality measures (eCQMs) on behalf of their clients under the "Direct EHR Submission" pathway. However, starting with the 2025 performance year, CMS has eliminated that option.
Now, only entities officially recognized as Qualified Registries (QRs) or Qualified Clinical Data Registries (QCDRs) can submit MIPS (Merit-based Incentive Payment System) quality data to CMS.
An EHR vendor wishing to continue submitting must go through the QR or QCDR qualification process — a rigorous, annual certification that includes extensive technical validation, data completeness reporting, and audit capabilities.
Why Did CMS Make This Change?
CMS outlined several reasons for tightening the submission process:
Data Integrity: By requiring Qualified Registry status, CMS ensures that submitted data meets higher accuracy and completeness standards.
Accountability: QRs and QCDRs must undergo yearly audits, ensuring consistency and validating the accuracy of submitted data.
Transparency: Qualified entities are held to reporting standards that EHR vendors historically were not, giving CMS greater visibility into how performance data is calculated and transmitted.
Simplification: Streamlining the submission pathways reduces administrative burden for CMS and clarifies submission expectations for providers.
In short, CMS is aiming to raise the bar for who can report on behalf of providers — making sure those entities are equipped to do so reliably.
What Does This Mean for EHR Vendors?
If an EHR vendor wants to continue offering data submission services for MIPS or other CMS quality programs, they must:
Apply to become a Qualified Registry (or partner with one).
Meet all technical requirements for measure calculation, data submission formats (such as QRDA III files), and performance feedback reporting.
Undergo annual validation and audits.
Support new measure types and evolving program requirements.
For many smaller or specialty EHR vendors, becoming a QR may be too resource-intensive. Some vendors are instead partnering with existing Qualified Registries to ensure their clients still have a path to successful CMS submissions.
Don't Wait Until Deadlines Are Looming
Contact us today to learn how ReportingMD can be your trusted partner in navigating the new CMS submission landscape.
What Does This Mean for Providers?
Providers can no longer assume that simply using an EHR system automatically enables CMS reporting. They must now:
Confirm whether their EHR is a Qualified Registry.
Evaluate alternative submission methods (such as contracting directly with a QR or QCDR).
Plan earlier for MIPS reporting deadlines, allowing time to establish submission partnerships if needed.
Failure to submit correctly could lead to penalties under MIPS, affecting a provider’s Medicare reimbursement rates.
What Should Organizations Do Next?
If you’re a healthcare organization, physician practice, or Accountable Care Organization (ACO), here are immediate action steps:
Ask your EHR vendor if they are a CMS-approved Qualified Registry for 2025.
Review your contract — does your current agreement include a CMS submission guarantee?
Start evaluating backup plans — such as contracting directly with a third-party Qualified Registry.
Stay informed — CMS often issues clarifications or additional guidance throughout the year. Make sure your compliance teams are monitoring updates.
Why ReportingMD is the Trusted Partner You Need
As a CMS-certified Qualified Registry for almost two decades, ReportingMD has the experience, technology, and healthcare expertise to ensure your organization remains compliant and achieves the best possible outcomes under MIPS and other value-based care programs.
We specialize in:
End-to-end data aggregation and submission across multiple EHRs and disparate systems.
Advanced quality analytics to help optimize your performance scores.
Comprehensive support through audit preparation, submission validation, and strategic guidance.
Proactive communication about CMS program changes so you are always prepared.
Whether you are a provider group, health system, ACO, or a vendor looking for a strategic partnership, ReportingMD can bridge the gap — delivering confidence, compliance, and improved financial results.
See the Impact Firsthand
Curious how partnering with a CMS-qualified registry can directly improve your performance outcomes? Download the Southlake Orthopedics case study to see how one organization significantly boosted its quality scores and reporting accuracy by working with ReportingMD. When compliance and performance matter, experience makes the difference.
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