How an in-house specialty pharmacy can leverage 340B programs and support covered entities (CEs)

By:  Zel Skrtic, PharmD
Chief Operating Officer of Specialty Pharmacy, CPS 

Published: August 2026

As seen in 340B Report

Regulatory turbulence is nothing new when it comes to 340B, but policy changes in areas beyond 340B have begun to indirectly impact the program, creating even more confusion, uncertainty, and complexity than before. 

This year, one such shift has impacted reimbursement for CEs as it relates to a large—and growing—population: Medicare patients.

Hot Topic: MFPs & 340B Discounts

Context & Impact

CMS-negotiated MFPs apply to a limited cohort of high-cost, high-utilization drugs covered under Medicare. However, the number of drugs with an MFP will expand over the next few years, totaling  2028,¹  so CEs will want to refine their process now before they have to scale an ineffective system into one that must account for even more medications.

The IRA-established MFP program requires manufacturers to reimburse pharmacies for the difference between their wholesale acquisition cost and the drug’s MFP within 14 days of submitting such claims to the Medicare Transaction Facilitator (MTF).²  During that same timeframe, CEs also need to determine the drug’s 340B eligibility,² effectively creating a tight deadline for an already difficult task. 

Why bother? If a drug qualifies for both MFP and 340B, then pharmacies receive only one discount for whichever has the lower price,² so timely identification is crucial.

Reality & Aftermath

Some CEs have encountered instances where manufacturers provide late MFP reimbursement, mistakenly assume 340B eligibility, or improperly deny the claim altogether.³  Since no mandatory appeal process or timeline exists to correct such errors, CEs reportedly have to cover a much higher purchase cost for an unknown amount of time.³

Even when the process works as intended, this new reimbursement structure can further decrease CEs’ limited financial liquidity while also increasing their operational strain and administrative burden. Ultimately, the extent of MFP’s impact is variable: CEs with a solid strategy will readily absorb the financial float, but those without may have to consider some serious sacrifices.

Proven Strategy: In-House Specialty Pharmacy

Context & Impact

MFP is just one component of the ever-evolving web of regulatory requirements all CEs must continuously manage. No matter the change, developing or growing a CE-owned specialty pharmacy is well positioned to overcome hurdles without compromising quality patient care.

On the surface, keeping specialty prescriptions in house can help ease the financial burden of prolonged reimbursement windows. The real impact is much deeper: in-house specialty pharmacy is now a more comprehensive, outcomes-driven initiative, making it an essential clinical partner in the treatment journey.

In-house specialty pharmacy can help CEs better adapt because of its unique clinical and operational attributes:

          →  Seamless integration within the same care continuum 

          →  Access to the electronic health record (EHR)

          →  Direct, on-site communication with patients and providers at the point of care

          →  Payor-specific expertise for an optimized prior authorization process

          →  Ongoing patient and therapy monitoring for better outcomes

          →  High-touch clinical outreach for greater treatment adherence 

Reality & Aftermath

Overall, success is influenced by integration depth, technology adoption, compliant 340B utilization, payor/manufacturer access, and data-informed decision-making. The latter should be an everyday commitment to continuously develop, implement, collect, assess, and evolve meaningful clinical and operational metrics that tell an actionable story.

At CPS, we showcase our data, benchmarks, and processes in an annual Patient Impact Report to help others elevate patient care, demonstrate value, and support growth. 

Click here to view the new 2026 Patient Impact Report.

Whether you want to evaluate investing in an in-house specialty pharmacy or you already have an established program, we can help. Our specialty pharmacy leaders and Apexus-Certified Experts (ACEs) work together alongside CEs of all types and sizes to help promote stability, realignment, and growth.

References

[1] US Centers for Medicare & Medicaid Services. Selected drugs and negotiated prices. US Dept of Health & Human Services. Updated May 22, 2026. Accessed June 24, 2026. https://www.cms.gov/initiatives/medicare-prescription-drug-affordability/overview/medicare-drug-price-negotiation-program/selected-drugs-negotiated-prices

[2] Seshamani M; US Centers for Medicare & Medicaid Services. Medicare Drug Price Negotiation Program: final guidance, implementation of Sections 1191-1198 of the Social Security Act for initial price applicability year 2027 and manufacturer effectuation of the maximum fair price in 2026 and 2027. US Dept of Health & Human Services. October 2, 2024. Accessed June 24, 2026. https://www.cms.gov/files/document/medicare-drug-price-negotiation-final-guidance-ipay-2027-and-manufacturer-effectuation-mfp-2026-2027.pdf

[3] DeCubellis J. Improving implementation of federal programs to reduce drug costs: feedback on progress in effectuating the maximum fair price and protecting 340B discounts. America’s Essential Hospitals. March 5, 2026. Accessed June 24, 2026. https://essentialhospitals.org/wp-content/uploads/2026/03/Deduplication-Issue-Letter-to-CMS.pdf