This guide was updated in August 2026 to reflect PY2026 MSSP ACO eCQM reporting requirements, APP Plus measure changes, and CMS quality reporting updates.
Is your Medicare Shared Savings Program (MSSP) ACO ready to tackle the complex world of Electronic Clinical Quality Measures (eCQM) reporting? While some organizations consider building their own internal reporting capabilities, the reality is that aggregating data from multiple EHRs, ensuring measure compliance, and preparing submission-ready files requires significant expertise and coordination that many underestimate. eCQM reporting for MSSP ACOs isn’t just a technical checkbox—it’s a high-stakes, data-driven operation that directly impacts your quality scores and shared savings potential.
This guide walks you through data acquisition, validation, aggregation, de-duplication, quality monitoring, and CMS submission via QRDA-III or FHIR JSON.
Have questions? Jump to our FAQ section for quick answers on CMS requirements, QRDA nuances, data strategies, and more.
What’s Changing for MSSP ACO eCQM Reporting in PY2026?
The measure set isn’t standing still, and this is the section to check every year before you plan your reporting build:
- The measure count is growing. ACOs reported six total APP Plus measures in PY2025 (four eCQMs/MIPS CQMs/Medicare CQMs, one administrative claims measure, and the CAHPS for MIPS Survey). That grows to eight measures in PY2026—five eCQMs/MIPS CQMs/Medicare CQMs plus two administrative claims measures—and CMS has finalized further growth to nine measures in PY2027 and 11 in PY2028.
- A fifth measure joins the set for PY2026: Colorectal Cancer Screening, alongside the four measures ACOs have already been reporting.
- PY2026 is the last year MIPS CQMs will be an option within the APP Plus quality measure set—if your ACO is still reporting MIPS CQMs, this is the year to finalize your transition to eCQMs or Medicare CQMs.
- The 40th percentile MIPS Quality Performance Category score for PY2026 is 73.85—the benchmark most ACOs need to clear (or exceed on the applicable outcome measures) to hit the maximum shared savings rate.
- CMS also streamlined the “reviewed” definition for the Colorectal Cancer Screening and Breast Cancer Screening measures, removing the requirement to document that screening results were discussed with the patient, and aligned age requirements across Breast Cancer Screening eCQM versions.
- The health equity benchmark adjustment is retired starting PY2026; CMS is leaning on the Complex Organization Adjustment and eCQM reporting incentives instead.
For a deeper look at how this fits into the broader 2026 Quality Payment Program changes, see MRO’s 2026 CMS Quality Reporting Changes guide.
What eCQMs and Quality Measures Must MSSP ACOs Report?
For performance year 2025, MSSP ACOs reported four specific eCQM/MIPS CQM measures as part of the APP Plus quality measure set:
- Diabetes: Hemoglobin A1c (HbA1c) Poor Control: the percentage of patients age 18–75 with diabetes whose most recent HbA1c is greater than 9.0%
- Preventive Care and Screening: Depression Screening + Follow-Up Plan: the percentage of patients age 12 or older who are screened for depression and, if positive, have a documented follow-up plan
- Controlling High Blood Pressure: the percentage of patients age 18–85 with diagnosed hypertension whose blood pressure is controlled (below 140/90 mmHg)
- Breast Cancer Screening: the percentage of women age 50–74 who received a mammogram every one to two years
Colorectal Cancer Screening joins this set for performance year 2026. Substance use disorder measures are slated to phase in for 2027, with social determinants and immunization measures expected in later years as the set grows toward 11 measures.
Step 1: Collect Clinical Data From Every Participating MSSP ACO Provider
Success begins with collecting structured clinical data from every provider (NPI) participating in your ACO. Given that practices often use different EHR vendors, there are usually inconsistencies in format and completeness that require strategic coordination:
- EHRs: all participating TINs must have a CEHRT version of their EHR for eCQM submission. Request QRDA-I files where possible, since these provide the most standardized format.
- Clinical Data Repositories (CDRs): leverage existing clinical data aggregation solutions to supplement clinical data across organizations.
- Alternative formats: when QRDA-I isn’t available or reliable, request FHIR, CCDA, or flat-file extracts (CSV, JSON) to ensure comprehensive data capture.
Early engagement with EHR vendors is critical to understand their capabilities, pricing structures, and limitations around extracting the right clinical data for CMS measures.
Step 2: Validate the Data Before You Trust It
Even structured data can be incomplete, and gaps can significantly impact your performance scores or make patients ineligible for measure inclusion. Comprehensive validation confirms you’re working with accurate, compliant information before it ever reaches an aggregation pipeline.
Step 3: Aggregate and De-duplicate Clinical Data Across EHRs
ACOs can use third-party platforms, build custom ETL pipelines, or adopt Common Data Models (like OMOP or FHIR) to unify clinical data from various EHRs. The goal is a standardized, longitudinal patient record for accurate reporting.
Duplicate patient records can inflate or skew quality measure calculations. Proper de-duplication ensures accurate numerator and denominator values, which directly affect an ACO’s quality scores and shared savings potential.
Step 4: Monitor Quality Continuously
Set up real-time dashboards that track each quality measure, provider performance, and time-based trends. Continuous monitoring helps identify data issues early and allows timely interventions before submission deadlines—rather than discovering a gap the week a deadline closes.
Step 5: Choose Your Submission Format: QRDA-III vs. FHIR JSON
- QRDA-III (XML)—CMS’s established submission format for aggregate data, widely supported by existing systems and vendors.
- FHIR JSON — a modern, API-based format aligned with CMS’s Digital Quality Measurement (dQM) initiatives, and the format CMS has signaled as the future direction of quality reporting.
Both are currently accepted. If you’re building new infrastructure from scratch, it’s worth weighing FHIR JSON even though QRDA-III remains the more broadly supported option today.
Step 6: Submit eCQM Data to CMS
- Utilize certified eCQM vendor tools (like MRO) for streamlined, compliant file creation.
- Develop custom scripts to convert cleaned data to QRDA-III XML using libraries like lxml (Python) or libxml2.
- Upload QRDA-III files directly to the Quality Payment Program (QPP) portal.
- Submit JSON files through FHIR APIs if your ACO has implemented direct reporting capabilities.
While building your own eCQM reporting pipeline offers control and customization, it’s also a complex, resource-intensive endeavor requiring technical expertise, dedicated infrastructure, and constant regulatory vigilance.
DIY MSSP ACO eCQM Reporting Checklist:
- Confirm every participating TIN has a CEHRT-certified EHR version
- Identify which practices can generate QRDA-I files vs. need alternative formats
- Map data elements from each source system and flag unmapped fields
- Run comprehensive validation for completeness and eligibility gaps
- Aggregate into a standardized, longitudinal patient record
- Run de-duplication before calculating numerators and denominators
- Stand up a real-time monitoring dashboard ahead of the submission window
- Decide on QRDA-III vs. FHIR JSON for your submission pathway
- Confirm whether your ACO is reporting eCQMs, MIPS CQMs, or Medicare CQMs for this performance year—and remember PY2026 is the last year MIPS CQMs are an option
- Submit through the QPP portal (QRDA-III) or FHIR APIs, with time to spare before the deadline
Let MRO Carry the Reporting Burden
Contact MRO today to learn how our comprehensive eCQM reporting solutions can help your ACO achieve optimal performance while maintaining focus on what matters most: delivering exceptional patient care.
FAQ’s on 2026 eCQM Reporting for MSSP ACOs:
What’s the difference between eCQMs, MIPS CQMs, and Medicare CQMs?
eCQMs pull structured data directly from certified EHRs across all patients and payers. MIPS CQMs are similar but calculated differently and are being phased out. PY2026 is the last year they’re an option under APP Plus. Medicare CQMs report only on ACO-assigned Medicare fee-for-service beneficiaries and serve as a transitional option for ACOs not yet ready for full eCQM reporting.
Is FHIR JSON required, or can we still use QRDA-III?
Both are currently accepted by CMS. QRDA-III remains the more broadly supported format today, while FHIR JSON aligns with CMS’s long-term digital quality measurement strategy.