CMS updates MIPS reporting deadlines: What practices need to know now

Physicians and practice administrators who participate in the Merit-based Incentive Payment System (MIPS) face a two-year lag between performance and payment that makes deadline awareness critical: what a practice does or does not submit today will show up as a payment adjustment on 2026 Medicare claims.

The 2024 performance year data submission window closed March 31, 2025, at 8 p.m. ET. Practices that missed the window or submitted incomplete data are now at risk of a downward adjustment of up to 9% on Medicare Part B payments.

The eCQI Resource Center confirmed the deadline and noted that CMS will release final 2024 MIPS scores in mid-June 2025, giving practices a window to review results before any appeals process.

For practices that submitted data through a third-party registry or qualified clinical data registry, confirming that the intermediary actually finalized the submission is an important step many administrators overlook. The filing deadline applies regardless of how data is submitted, meaning a registry delay or technical error on the registry's end can still result in a penalty if it goes unresolved. The QPP portal at qpp.cms.gov allows practices to verify submission status directly and review any data submitted on their behalf.

Practices that believe they qualify for a hardship exception or an extreme and uncontrollable circumstances waiver have a separate application process through the QPP website. CMS has historically granted exceptions for significant electronic health record (EHR) transitions, natural disasters, and certain public health emergencies. Each application is reviewed on a case-by-case basis, and documentation of the qualifying circumstance is required. The QPP Resource Library includes updated guidance on exception eligibility, application instructions, and a performance feedback dashboard that shows where a practice's score currently stands.

Reporting structure is another area where practices sometimes leave points on the table. Physicians who submitted as individuals rather than as a group, or vice versa, may have received a different score than they would have under the alternative option. CMS assigns the highest available score when a clinician has multiple final scores from different participation options, but only if both submissions were made. Practice administrators should review their participation structure annually rather than defaulting to whatever option was used in the prior year.

Small practices, defined as 15 or fewer eligible clinicians, may also qualify for the small practice bonus, which has added up to 5 percentage points to final MIPS scores in recent program years. That designation is determined by CMS based on claims data, but practices that believe they qualify and are not seeing the bonus reflected in their score should review their eligibility status through the QPP participation lookup tool.

Looking ahead, CMS has signaled that the traditional MIPS reporting framework may be phased out as early as 2027 in favor of MIPS Value Pathways (MVPs), which require specialty-specific reporting by subgroup. Practices that have not yet evaluated which MVP applies to their clinicians should do so before the 2025 performance year is fully underway.

The QPP helpdesk at 1-866-288-8292 is available Monday through Friday, and the CMS Quality Payment Program overview page covers the full structure of both participation tracks.

One area where practices consistently leave points behind is the Promoting Interoperability (PI) category, which rewards the use of certified EHR technology for specific functions including e-prescribing, patient access to health information, and electronic referral loops. Practices that have not reviewed their PI reporting in the past year may be missing credit for workflows already in place.

An EHR vendor or a certified health IT consultant can help identify which PI measures a practice is already meeting and where additional documentation could improve the score.