Federally Qualified Health Centers

AAFCPAs has provided strategic and pragmatic CPA and advisory solutions to FQHCs since our founding in 1973.

Audit, Consulting, and Tax for Federally Qualified Health Centers

AAFCPAs has extensive experience with financial and operational issues impacting FQHCs, including federal, state, and local government funding, Medicaid and Medicare reimbursement, telehealth, behavioral & dental health, the federal 340B drug pricing program, and more. We provide clients with a deep bench of expertise offering specialized consulting & reimbursement solutions, audits, tax planning & compliance.

How may we help you?


AAFCPAs has provided CPA and advisory solutions to FQHCs and FQHC networks throughout the United States since our founding in 1973.

We have comprehensive experience with audits in accordance with Uniform Guidance / Single Audits, Financial Accounting Standard Board Requirements, state-specific financial reports, as well as organizations with employee benefit plans subject to ERISA compliance requirements.

We have expertise with the policies, procedures, and regulations related to healthcare accounting and financial requirements at all levels, including the U.S. Department of Health and Human Services (HHS), Centers for Medicare and Medicaid Services (CMS), state Departments of Public Health, and other state grant management agencies.

340B Pharmacy Program Audits and Consulting

AAFCPAs’ Healthcare practice has deep expertise in the federal 340B Drug Pricing Program compliance. We help clients:

  • Successfully prepare for an Office of Pharmacy Affairs (OPA) audit,
  • Ensure 340B Program integrity and maintain accurate records documenting compliance with all 340B Program requirements, and
  • Mitigate major risks associated with the 340B Program.

Learn more about our 340B Pharmacy Program Audits and Consulting.>>

CFO/Controller Advisory

AAFCPAs provides a full range of outsource accounting and advisory services, including high level Controller and CFO solutions. These include financial statements, comparative reporting, budgeting, financial strategy & modeling, and market analysis.

We are fully equipped to assume a lead role in exploring and implementing means of managing and improving the financial performance of your organization.  We may also assist with the oversight of internal controls, all areas of receivables management, standards implementation, and other systems and procedures to achieve efficiencies in your business office.

Our extensive experience serving FQHCs allows our staff to provide the types of industry-specific business insights our clients need.  We are intimately familiar with FQHC financial processes, risk factors, patient populations, KPIs, and regulatory environment. Learn more about AAFCPAs’ Outsourced Accounting & Fractional CFO Solutions >>

Business Process & IT Consulting

AAFCPAs’ integrated Business Process & IT Consulting practice provides Productivity Improvement, Business Intelligence, and IT & Cyber Security solutions.

We advise FQHCs on improving revenue cycle processes and optimizing IT systems. We provide operational process reviews and robotic process automation solutions related to billing and collection, accounts receivable management, reserve analysis, fee schedule analysis, business process improvement, and recommendations for implementing denial management processes.

We help clients transform data into actionable insights. We leverage specialized skills, state-of-the-art technologies, and proven methodologies to extract, inspect, cleanse, and model data in order to discover meaningful information that supports better decision making.

We help FQHCs protect their patients’ personally identifiable information! We help identify risks that could potentially cause information loss or financial or reputational harm. Our solutions include IT & Cyber Security Assessments, Vulnerability Management as a Service (VMaaS), and HIPAA compliance certifications. Learn more.>>

Learn more about AAFCPAs’ Business Process & IT Advisory Solutions.>>

Revenue Cycle Management Services

In addition to best value assurance and tax expertise, AAFCPAs provides specialized advisory services for FQHCs to optimize reimbursements, including:

Revenue Cycle Assessments

AAFCPAs performs internal control reviews of the revenue cycle operation to help clients capture more revenue. This involves assessing the controls and procedures from the front end through the back, and all the various layers in between in the collection of accounts receivable. We perform analysis of your insurance verification process, authorization & re-authorization process, timing of billing, and collection follow-up. We take an objective and subjective look at your people, process, and technology and make pragmatic and best practice recommendations in areas where FQHCs may increase reimbursement and improve revenue cycle management efficiency.

Fee Structure Analysis

We review current medical, behavioral health, and dental fee structures to determine adequacy of rates charged and make rate setting recommendations to ensure optimal reimbursement.

Sliding Fee Discount Program Assessments

AAFCPAs assist clients in calculating medical rates and optimizing collection based on the HRSA’s Sliding Fee Discount and Related Billing and Collection Program Requirements. We ensure clients maintain organizational compliance, which includes documentation of policies and procedures to meet HRSA’s program requirements. We help clients avoid issues associated with an HRSA Operational Site Visit.

Medicaid and Medicare Cost Reporting

AAFCPAs has extensive cost reporting and reimbursement experience with both cost-based and Prospective Payment System (PPS) providers. We understand the importance cost reports hold for FQHCs. We provide guidance to ensure accurate completion, insight into the key objectives of the report, and critical areas of scrutiny of your disclosures. We frequently present training sessions to FQHC associations on best practices for minimizing the effort necessary to prepare, while maximizing reporting to properly reflect your true cost of care and maximize reimbursements.

Denials Prevention and Management

Most denials are caused by inefficient processes and can be prevented. Denials can be caused by internal issues, technology issues, or billing complications from third party payors. Interpreting the billing and coding requirements of a variety of payors can be challenging. AAFCPAs identifies opportunities to minimize denials and increase reimbursement. This includes identifying the causes for the denials and common themes. If the denials are caused by internal factors, we can provide training to prevent the denials from reoccurring. If the denials are caused by external payor issues, we work with clients to develop an action plan to address these with the insurance companies. We utilize our Data Analytics team as well as advanced, data mining software as appropriate to enhance our abilities to evaluate vast amounts of data found within complex, disparate information systems.

Dashboarding & KPIs

AAFCPAs helps FQHCs monitor the health of their revenue cycle with data analysis and visualization. This includes guidance on the appropriate metrics, or key performance indicators (KPIs), that inform your decision making. Our in-house data analysts work with your team to extract, inspect, cleanse, and model data in order to monitor real time the health of your revenue cycle operations.

Healthcare Consolidation & Coordination of Care

AAFCPAs has witnessed dramatic changes in the healthcare industry, including the current consolidation landscape and integration of behavioral health into the primary care delivery system.  Our specialists are well-prepared to advise clients on forging innovative partnerships or consolidations that will improve the quality of care and clinical outcomes while controlling costs.  We help clients to perform well-executed integrations that optimize both outcomes and profitability. This includes:

  • Vetting potential healthcare partnering arrangements, including comparative analysis of competition, cost structures & payment methods, practice patterns, quality of care, and clinical outcomes.
  • Guidance on changes in reimbursement and regulatory frameworks and the increased proliferation of high-deductible health insurance plans.
  • Analysis of Accounts Receivable & Third-Party Reimbursement.
  • Optimizing ROI on technological investments and aligning business process controls with performance objectives.
  • Guidance on improving processes and leveraging systems to streamline reporting and compliance requirements.
  • Development of tracking and monitoring systems for risk-based contracts. This involves determining the costs for providing the services to be covered under the contract. In addition, we also help to develop a system to monitor the services being provided and costs involved. The profit/loss on these contracts needs to be determined as well as how much is attributable to the organization. We consult on the level of reserves that are necessary for these contracts, and the accounting and financial reporting requirements.

Tax & Tax Credit Transactions

We are instrumental in helping FQHCs fund new capital initiatives with various tax credit programs. Our comprehensive knowledge of all new, existing, and changing applicable tax credits includes New Markets tax credits, federal and state Historic Rehabilitation tax credits, tax credit exchange, tax credit assistance programs, and credits for use of alternative energy sources.

We provide advisory services to limited partnerships/limited liability companies from cost certifications at the project’s inception, to exiting at the end of tax credit compliance periods.

We also assist tax exempt organizations like FQHCs in optimizing the presentation for your Forms 990 to donors and the public.

What our clients say…

Contact AAFCPAs

We look forward to speaking with you to determine how we may best solve your needs. A firm representative will reach out to your within one business day. Looking for additional ways to reach us? Visit our Contact Page. >>