Medicare CQM Implementation Timeline: A Practical Checklist for ACOs

Successfully implementing Medicare CQMs for the APM Performance Pathway (APP) requires careful planning and execution throughout the year. This implementation guide will help your ACO navigate the transition from the Web Interface to Medicare CQM reporting while ensuring you’re prepared for the eventual move to all-patient, all-payer quality measurement.

Understanding the Medicare CQM Timeline

Medicare introduced Medicare CQMs in 2024 rulemaking as a temporary bridge to help ACOs transition from the Web Interface to the more demanding technical requirements of all-patient, all-payer reporting. Unlike MIPS submitters who have reported on all patients of all payers since 2017, ACOs can use Medicare CQMs to report on a smaller, more manageable patient population: only Medicare Part B beneficiaries who have seen a primary care provider in your ACO during the performance year.

This timeline assumes you’re planning for a performance year that ends December 31st, with a submission deadline in late March of the following year.

Months 1-3: Foundation & Assessment Phase

Understand Your Options and Set Your Strategy

Key Activities:

Review your current quality reporting approach:

Document which collection methods you’re currently using

Identify what’s working and what challenges you’re facing

Review your most recent quality scores and percentile rankings

Understand Medicare CQM fundamentals:

Medicare CQMs use the same specifications and methodology as MIPS CQMs

Measure specifications are only available for the submittable measures of the APP

Numerator and denominator specifications are identical to MIPS CQM counterparts

The only important difference from MIPS CQMs is the eligible patient population (Medicare Part B only vs. all-patient, all-payer)

Assess your potential Medicare CQM population size:

Understand that nationwide, approximately 12% of adults seeing a healthcare provider are Medicare recipients

In practices serving Medicare patients, about 30% of the patient population tends to be Medicare (varies by specialty and practice dynamics)

Estimate your Medicare Part B population across all participating practices

Determine if Medicare CQMs make sense for your ACO:

If you’re working with electronic data, analyzing 300 Medicare Part B patients vs. 1,000 all-payer patients requires nearly the same effort

If you need manual chart abstraction to improve reporting accuracy, Medicare CQMs make the task significantly easier due to lower patient counts

Medicare CQMs are particularly valuable if you have a large all-patient population that makes complete eCQM reporting challenging

Organize Your Payer Data Infrastructure

Key Activities:

Begin comprehensive payer data collection:

Identify that your ACO may have thousands of different payers across the entire enterprise

Create a systematic process to collect payer information from all participating practices

Document all payer variations, names, and identifiers currently in your systems

Categorize payers correctly:

Organize all payer data into Medicare and non-Medicare categories

Filter specifically for Medicare Part B coverage

Create validation rules to ensure consistent categorization across practices

Map patients to participating practices:

Identify which TIN-practices are participating in your ACO

Ensure you can connect each Medicare Part B patient to the practices where they were seen

Verify primary care provider encounters for eligibility

Document your data sources:

Inventory all EHR systems across participating practices

Identify claims data sources

Document any data gaps or challenges in specific practices

Initial Population Validation

Key Activities:

Access the CMS quarterly patient file:

Medicare provides a quarterly list of patients who might qualify for Medicare CQMs

Request access to the first quarterly file (typically available early in Q1)

Use the quarterly file as a validation tool:

Compare the CMS file population size to your internal estimates

Identify any significant discrepancies that might indicate under-reporting

Note: The quarterly file is valuable for validation but has limitations for actual reporting

Validate your population size assumptions:

Confirm you’re identifying the right Medicare Part B patients

Check that your population size aligns with expected percentages

Document any practices where you’re having difficulty identifying the Medicare population

Establish baseline performance metrics:

If possible, run preliminary analytics on available data

Identify which measures may need additional manual chart abstraction

Estimate the effort required for data completeness

Months 4-6: EHR Vendor Assessment & Data Collection Setup

Evaluate EHR Vendor Capabilities

Key Activities:

Determine if your EHR vendor will support Medicare CQM submission:

It’s possible for an EHR to submit Medicare CQMs, but they must function as a qualified registry

This is more credible if you have only one instance of one EHR in your ACO

Note that EHR vendors face significant challenges to deduplicate and identify patients across multiple practices and connect them to clinical numerator data

Ask critical questions of your EHR vendor:

Question 1: Are you a qualified registry?
- If they’re not a qualified registry, they’re unable to support Medicare CQMs

- For eCQM submissions, they only need ONC certification (not qualified registry status)
Question 2: How will you identify and deduplicate patients across multiple practices?
- The answer must be a credible technique as different EHRs do not generally play well together and ACOs usually have multiple EHRs and participating practices
Question 3: How will you normalize the clinical numerator data to generate metrics across all EHRs in your ACO?
- This is critical for accurate reporting across diverse systems

- Ask for specific examples of how they handle data from different EHR platforms
Question 4: How will you deal with missing data?
- If critical information was recorded but not in a way the EHR could find it, what’s their solution?

- Understand their process for identifying and addressing data gaps

Make a decision on EHR vendor involvement:

Determine if your vendor can credibly support Medicare CQM reporting

If not, plan for alternative reporting solutions (qualified registry partner, self-submission, etc.)

Set Up Data Collection Processes

Key Activities:

Establish your data collection methodology:

Decide whether you’ll use any method available for MIPS CQMs (including manual methods and non-certified data sources)

Remember: For eCQMs, you can’t use manual methods or non-certified data sources, but Medicare CQMs offer this flexibility

Plan which measures will require manual chart abstraction

Access the second quarterly CMS file:

Continue validating your population identification

Compare Q2 file to your internal tracking

Identify any trends or persistent gaps

Begin systematic eligibility confirmation:

You cannot take Medicare’s eligibility determinations for granted

Establish processes to confirm eligibility using service codes and ICD codes

Verify that patients were seen by primary care providers in your participating practices

Connect patients to their clinical numerator data

Test your data extraction processes:

Run test extractions from all EHR systems

Identify technical challenges or data quality issues

Document workarounds for problem areas

Establish data quality checkpoints:

Create validation rules for numerator data

Set up processes to identify missing or incomplete clinical information

Determine which measures will benefit most from manual chart review

Plan for Data Completeness Requirements

Key Activities:

Understand the 75% data completeness requirement:

Medicare CQM reporting requires 75% of eligible patients to be included in your submission

Some member practices may present challenges for data collection—this threshold makes the process more manageable

Identify practices with data collection challenges:

Document which practices have limited technical capabilities

Note practices where you’re having difficulty extracting data

Calculate your expected data completeness percentage

Develop contingency plans:

If certain practices cannot provide data, ensure you’ll still meet the 75% threshold

Consider which practices are most critical to include

Plan additional manual abstraction if needed to reach completeness goals

Set up ongoing monitoring:

Establish quarterly check-ins on data completeness

Create alerts for practices falling behind

Build in time for remediation activities

Months 7-9: Mid-Year Performance Review & Optimization

Mid-Year Performance Assessment

Key Activities:

Access the third quarterly CMS file:

Continue population validation with the Q3 file

Compare your year-to-date data capture against CMS expectations

Run mid-year performance analytics:

Calculate performance on all intended submission measures

Identify measures where you’re scoring well vs. those needing improvement

Assess your progress toward data completeness:

Calculate current percentage of eligible patients with complete data

Identify gaps that need to be addressed in Q4

Prioritize practices or measures needing additional attention

Review manual abstraction needs:

Determine which measures would benefit from manual chart review

Estimate the volume of manual work required

Score Optimization Planning

Key Activities:

Understand how Medicare CQMs affect your scores:

Your comparison group for Medicare CQMs is restricted to other ACOs (not all practices in the US)

Typical ACOs perform better in real terms because they’re more focused on quality performance and invest more resources

Good quality performance is essential for collecting shared savings

Consider the flat benchmark advantage:

Medicare is establishing flat benchmarks for Medicare CQMs until historical benchmarks are available in the third year

For the first two years, you’ll have clarity on your possible scores at any performance rate

Use this to set realistic targets

Evaluate whether to submit multiple collection types for the same measure:

Remember: You can submit the same measure via Medicare CQMs, MIPS CQMs, and eCQMs

Medicare will credit you with the best score from redundant submissions

Calculate whether the additional effort is worth the potential score improvement

Plan your Q4 improvement initiatives:

Identify specific interventions to improve performance on low-scoring measures

Focus manual abstraction efforts where they’ll have the greatest impact

Engage clinical teams in targeted quality improvement

Final Preparation Phase Begins

Key Activities:

Access the fourth quarterly CMS file:

Note: This file comes late (typically not until October)

It may be too late to comfortably use for full-year submission planning

Continue using it primarily for validation, not as your denominator source

Lock in your submission strategy:

Finalize which measures you’ll submit and via which collection methods

Confirm your EHR vendor’s role (if any) in the submission

Document your complete submission plan

Prepare for Q4 data collection:

Ensure all systems are functioning properly

Brief all participating practices on final quarter expectations

Set up processes to capture Q4 data efficiently

Begin preliminary submission file preparation:

Start organizing data in submission-ready formats

Test submission file generation if using registry pathways

Identify any technical issues that need resolution

Months 10-12: Final Data Collection & Quality Assurance

Q4 Data Collection & Quality Focus

Key Activities:

Monitor real-time performance:

Track Q4 performance trends

Identify any unexpected drops or issues

Make mid-course corrections as needed

Validate patient eligibility continuously:

Continue confirming eligibility using service codes and ICD codes

Ensure patients are correctly mapped to practices

Verify primary care provider encounters

Data Finalization

Key Activities:

Complete Q4 data extraction:

Extract all clinical data from EHR systems

Compile claims data from all sources

Identify and address any final data gaps

Conduct final population validation:

Review complete year’s patient population

Confirm you’ve captured all eligible Medicare Part B patients

Verify data completeness percentage meets or exceeds 75%

Execute manual chart abstraction:

Complete all planned manual chart reviews

Focus on measures where manual abstraction will most improve scores

Run preliminary final analytics:

Calculate performance across all measures

Compare multiple collection methods if you’re submitting redundantly

Identify your best scores for each measure

Quality check all data:

Validate numerator and denominator calculations

Check for data anomalies or outliers

Confirm all clinical data meets measure specifications

Pre-Submission Review

Key Activities:

Complete all data collection:

Finalize year-end data extraction

Close out any pending manual abstraction

Conduct comprehensive data validation:

Review eligibility confirmations

Verify patient deduplication across practices

Confirm clinical numerator data accuracy

Generate final performance reports:

Calculate final scores for all measures

Compare against measure benchmarks

Document your expected percentile rankings

If using multiple collection methods, compare final scores:

Determine which collection method yields the best score for each measure

Plan to submit the optimal combination

Prepare submission files:

Generate files in required formats

Validate file structure and content

Test file uploads if submitting electronically

Months 13-15: Submission Period

Final CMS File Review & Submission Prep

Key Activities:

Review final year-end performance:

Analyze complete year results

Identify any last-minute opportunities for score improvement

Document lessons learned for next year

Prepare submission documentation:

Compile all required supporting materials

Document your methodology and data sources

Prepare attestations as needed

Conduct final quality assurance:

Check all calculations

Verify data completeness percentages

Confirm all measure specifications were met correctly

Test submission processes:

If using a qualified registry, confirm they’re ready

Test file uploads and system connections

Resolve any technical issues

Final Adjustments

Key Activities:

Access the final CMS quarterly file:

Note: This file typically arrives in February

It’s late for comfortable use in your full-year submission

Use it only for final validation if needed

Make final submission decisions:

Finalize all performance calculations

Approve submission files for upload

Prepare for submission deadline:

Confirm exact submission deadline (typically mid-March)

Create backup plans for technical issues

Submit to CMS

Key Activities:

Submit your quality measures to CMS:

Upload final submission files

Verify successful submission receipt

Save all confirmation documentation

Conduct post-submission review:

Document what worked well

Identify challenges for next year’s implementation

Begin planning improvements for the next performance year

Brief teams on next steps:

Explain when results will be available

Discuss timeline for benchmarking and scoring

Plan for continuous quality improvement

Planning for the Transition to All-Patient, All-Payer Reporting

While implementing Medicare CQMs, begin preparing for the eventual transition:

Build infrastructure for all-payer data collection:

Even while using Medicare CQMs, continue developing systems to capture all-patient data

Test your ability to identify and categorize all payers

Gradually expand your data collection capabilities

Invest in technology and processes:

Consider whether registry partners can help with the transition

Evaluate EHR optimization opportunities

Build team capabilities for more complex reporting

Monitor CMS rulemaking:

Stay informed about potential changes to the APP

Watch for announcements about Web Interface sunset timing

Adapt your strategy as regulations evolve

Getting Support for Your Implementation

Choose a Registry Partner with APP Experience

In the transition to APP reporting, your ACO has important decisions to make that could impact your performance and shared savings. As a Qualified Registry with over a decade of experience reporting to CMS, Mingle Health eases the transition to APP reporting for ACOs while helping them improve processes and performance. With Mingle Health, ACOs gain access to valuable tools, experience, and a proven track record of quality reporting for organizations of all sizes and technical abilities.

With Mingle Health, your ACO gains access to:

Data expertise to combine your data from multiple sources while providing a complete view of quality measure performance across locations and EHRs.
Flexibility in collection methods with our support for eCQM, MIPS CQM, and Medicare CQM reporting.
A dedicated Mingle Health Consultant that understands your ACO’s specific challenges and needs while helping you navigate current and future reporting requirements.
Tools and guides to ensure your ACO is meeting APP requirements and creating the best quality submission possible with your challenges, needs, and technical landscape.
Communication assistance and consulting to ensure that ACO member practices understand the new APP reporting requirements and how they will be affected.