Beyond the Counter

The Hidden War Between Independent Pharmacies and PBMs

Independent pharmacies have long been the backbone of community healthcare, especially in rural and underserved areas. But as we navigate through early 2026, these small businesses are facing an existential “squeeze” from the massive entities that control the flow of prescription drugs. As operational pressures grow, independent pharmacies are increasingly turning to reliable pharmacy packaging solutions and cost‑effective prescription packaging supplies to stabilize workflow and protect shrinking margins.

While recent federal legislation, like the Consolidated Appropriations Act of 2026 signed this February, has finally begun to tackle Pharmacy Benefit Managers (PBM) reform by “delinking” profits from drug prices, independent pharmacists are still fighting an uphill battle against decades of predatory practices. Here are the primary challenges keeping your local pharmacist up at night.

The “Under-Water” Reimbursement Crisis

The most immediate threat to an independent pharmacy’s survival is negative reimbursement. This is a phenomenon where Pharmacy Benefit Managers (PBMs) reimburse pharmacies at rates lower than the actual cost of purchasing the drug from a wholesaler. PBMs are the “middlemen” of the healthcare industry. They act as the central hub between health insurance companies, drug manufacturers, and pharmacies. While they were originally created to process paperwork, they now essentially dictate which drugs you can get and how much you pay for them.

For these small businesses, every prescription filled under this model is a financial liability. They are essentially “paying” for the privilege of serving their community. With reimbursement cuts eroding profitability, every piece of the pharmacy’s workflow matters, from staffing to inventory to efficient medication packaging systems that minimize waste and streamline dispensing. This persistent margin compression has contributed to a devastating closure rate of roughly one independent pharmacy per day across the U.S. While the new 2026 laws strengthen “Any Willing Pharmacy” rules to stop PBMs from blocking independents from their networks, the struggle for fair pay remains. Access to a network doesn’t mean much if the contract is a “take-it-or-leave-it” deal that doesn’t even cover the light bill.

Vertical Integration and “Patient Steering”

Independent pharmacies aren’t just competing with other stores. They are competing with their own payors. The “Big Three” PBMs—CVS Caremark, Express Scripts, and OptumRx—are vertically integrated giants that own the very retail, specialty, and mail-order pharmacies they want you to use.

This creates a massive conflict of interest. PBMs often use aggressive “patient steering“ tactics, like requiring you to use their mail-order service for chronic meds or hitting you with higher copays if you choose to visit the independent shop down the street. These maneuvers drain the customer base of local pharmacies to pad corporate pockets. While the Break Up Big Medicine Act, introduced in early February 2026, aims to stop this and is currently a heavy lift in a divided Congress.

The End of DIR Fees (and the New Cash Flow Crunch)

For years, PBMs used Direct and Indirect Remuneration (DIR) fees. Essentially, retroactive “clawbacks” taken months after a drug was already sold. This kept PBM profit margins high and pharmacy owners guessing.

Recently, regulatory changes moved these fees to the “point of sale” to increase transparency. In the long run, while great, it created what is called the “DIR Hangover” or the “Cash Flow Cliff.” In late 2025 and early 2026, many pharmacies were stuck paying off old retroactive fees while simultaneously receiving lower upfront payments under the new rules. Many local pharmacists are still reeling from this liquidity crunch, trying to find the cash to keep high-cost medications on the shelves while waiting for reimbursements that barely cover their costs. During these cash‑flow crunches, pharmacies often seek out affordable pharmacy supply partners to reduce daily operational costs without compromising quality.

Aggressive Audits and Administrative Burden

You’ve probably heard of a tax audit, but for independent pharmacists, a PBM “desk audit” is a whole different level of stress. These aren’t just routine check-ins. They’ve become an aggressive revenue recovery tool where PBMs hunt for tiny clerical errors to justify taking money back.

These are cases where an auditor might claw back the entire cost of a $10,000 life-saving medication just because of a slightly smudged signature or a missing date on a digital form. It feels less like quality control and more like a “gotcha” game. On top of that, trying to get specialty drugs to patients feels like an administrative marathon of Prior Authorization paperwork and Step Therapy hurdles. It’s a massive drain on staff time that should be spent with patients, leaving people waiting in limbo while the pharmacy fights a paperwork war.

Despite the daunting “squeeze” of underwater reimbursements and corporate gatekeeping, there is a sense of cautious optimism as we move through 2026. The passage of the Consolidated Appropriations Act this February marks a historic turning point, signaling that the “Wild West” era of opaque PBM practices is finally being reined in by federal law. While independent pharmacists are still navigating the fallout of the “DIR fee hangover” and aggressive audits, they are no longer fighting in the shadows. With new transparency mandates, “Any Willing Pharmacy” protections, and a growing public demand for personalized, community-based care, the tide is starting to turn. Independent pharmacies aren’t just surviving. They are redefining their value as essential healthcare hubs that offer something no mail-order algorithm ever could – a real relationship with a trusted professional.

As independent pharmacies continue fighting for fair reimbursement, transparency, and the ability to care for their communities without interference, having reliable operational partners has never mattered more. At Samuels Products, we understand the pressures local pharmacies face, and we’re committed to supporting their work with efficient, and cost‑effective pharmacy packaging solutions that streamline workflows and protect their bottom line. If your pharmacy is looking for packaging you can depend on, reach out to Samuels Products to learn how we can help strengthen your operations in this challenging PBM landscape.