Read this if you are a CEO, CFO, or COO at an FQHC.
This article is the first in a three-part series to help Federally Qualified Health Centers understand how site- and program-specific accounting is essential to sustainability. Next up: How FQHCs can refine accounting to improve their bottom line
Federally Qualified Health Centers (FQHCs) face a perfect storm: level grant funding, shrinking 340B savings, and rising expenses. Staying sustainable requires identifying ways to maximize operations and revenue while controlling costs. That’s where site- and program-specific accounting becomes essential.
Traditionally, FQHCs produce financial statements that present revenues, expenses, and the bottom line at the organization-wide level. However, for FQHCs with multiple sites and programs, which is most of them, this approach can mask high-performing or underperforming sites and services. By modifying accounting methods to take a more granular look at performance, management can uncover what is working and what is not to improve overall operations.
Site-specific accounting for FQHCs
For FQHCs with multiple locations, site-specific accounting provides critical visibility into how each site is performing. If one site is doing well, a closer look at its practices can reveal strategies to replicate across other locations. Without tracking income statements by site, these insights remain hidden.
Program-specific accounting for FQHCs
Similarly, program-specific accounting allows management to understand the profitability and cost structure of each service line, whether medical, dental, behavioral health, or enabling services, across all delivery sites. Because most FQHCs offer multiple programs at every location, program-specific accounting ensures that profitable programs can subsidize those operating at a loss, supporting the health center’s mission to provide comprehensive, community-responsive care.
The bottom line for health centers
A significant portion of FQHC reimbursement comes from the Health Resources and Services Administration (HRSA). Although HRSA has occasionally provided supplemental funds for program expansions such as behavioral health or dental care, the base grant funding has not increased since 2015. This funding stagnation, coupled with rising expenses, has created a growing gap and margin compression.
A key element of FQHC sustainability is the 340B Drug Pricing Program, which was created to help eligible providers stretch scarce federal resources as far as possible, reaching more eligible patients and providing more comprehensive services. For many FQHCs, 340B savings have been critical to bridging the gap between costs and reimbursements. In 2019, every dollar through the program generated an average of 65 cents in net savings for health centers. However, in 2020, an Executive Order restricted HRSA’s oversight of the program, enabling drug manufacturers to impose their own restrictions. As a result, margins fell to an average of 45 cents per dollar in 2024. These shrinking savings directly reduce the funds FQHCs rely on to maintain comprehensive services and sustain operations, making it harder to cover costs, particularly for unprofitable programs that still fulfill vital community needs.
With the loss of COVID-19 supplemental funds, diminished 340B savings, and rising expenses, many FQHCs now face a negative bottom line for the first time. This underscores the urgent need for site- and program-specific accounting to identify and address areas of weakness and opportunity.
Obstacles to changing accounting structures
Historically, FQHCs have operated on very tight budgets. Many centers began small with lean finance teams to control overhead. In the past seven to eight years, as FQHCs have grown in size and scope of services, their finance teams have not always expanded proportionally. As a result, these teams often lack the resources to revise the chart of accounts or implement new tracking methods. Now, with costs exceeding reimbursements, identifying site and program performance is essential for survival.
Taking the next step
Adopting site- and program-specific accounting isn’t just an operational improvement; it’s a strategic imperative in the face of rising costs and shrinking margins. By identifying what’s working and what needs adjustment, FQHCs can make data-driven decisions to strengthen their bottom line, safeguard their mission, and continue serving their communities effectively. For health centers navigating today’s challenges, granular accounting insights are not just helpful, they’re essential for resilience and long-term sustainability.
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