The first half of 2025 delivered a clear message to independent pharmacies: PBM audits are more aggressive, more technical, and more unforgiving than ever. Pharmacies face greater operational and legal risks under increasingly one-sided audit practices.  This article draws from recent client experiences and highlights the most notable trends in PBM audit enforcement, common triggers fueling audit exposure, and key strategies pharmacies must implement now to minimize disruption, defend against recoupments, and preserve network participation.

Audit Volume is Up, and so is Enforcement Pressure

PBMs dramatically increased the number of audits conducted in 2025. Pharmacies of all types – particularly those submitting higher-cost claims – find themselves on the receiving end of document requests and demand letters.  What separates 2025 from prior years is not just the volume of PBM audits, but the rigidity with which PBMs enforce technical standards.  Even historically acceptable documentation or those with minor variances are rejected, leading to higher discrepancies and chargebacks.  Heightened enforcement posture contributes to a significant uptick in recoupment demands, with some PBMs initiating network terminations based solely on alleged audit findings. 

Common Audit Triggers: Where Pharmacies are Being Targeted

While PBMs continue to cite fraud, waste, and abuse as the basis for their audit programs, the reality is that most audit findings in 2025 stem from routine, often unintentional discrepancies in documentation or billing. One increasingly common trigger involves discrepancies in National Drug Code (NDC) reporting.  PBMs treat claims submitted with a different NDC than what appears on the pharmacy’s purchase invoice as a red flag – even if the medication dispensed is therapeutically identical and properly labeled. These findings, often the result of wholesaler substitutions or system-generated data mismatches, are nonetheless characterized as overpayments.

The adequacy of supporting documentation is another area of concern for independent pharmacies.  Pharmacies that do not produce complete dispensing records, purchase invoices, or delivery confirmation documentation receive citations for “material noncompliance,” even in cases where the underlying transaction is otherwise legitimate.  The evidentiary burden imposed by PBMs has shifted. PBMs expect pharmacies to meet increasingly narrow documentation standards, and failure to do so – even in isolated instances – results in disproportionate penalties, including recoupment and even network terminations. 

In a more alarming trend, PBMs are also auditing performance metrics tied to Direct and Indirect Remuneration (DIR) fees.  PBMs flag pharmacies that fail to meet certain thresholds, such as adherence scores or other quality-based metrics, for deeper audit reviews.  This development is troubling on several levels, as it allows PBMs to leverage performance-based outcomes as a pretext for broader financial recovery.

Strategies for Defending Against and Preventing PBM Audit Findings

Pharmacies must take a proactive stance in light of the mid-year audit landscape.  The first step in a proactive approach is ensuring that all documentation is maintained in a complete and audit-ready format.  Purchase histories must match the NDCs submitted on claims.  Signature logs, delivery confirmations, and prescriber records must be organized and readily accessible.  Pharmacies cannot rely on the assumption that “close enough” will suffice – it won’t.

Pharmacies are encouraged to conduct internal audits and claim reviews on a rolling basis in preparation for PBM audits.  Rather than waiting for a PBM to identify potential discrepancies, pharmacies must self-identify and correct issues in advance.  Internal audits may involve reviewing claim histories for high-cost products, reconciling purchase records, or validating proof of delivery and receipt by the appropriate patient. 

In addition, when an audit is initiated, it is critical that pharmacies seek legal counsel before submitting documentation or responding to initial audit findings.  Legal counsel can assist in interpreting the provisions of PBM Provider Manuals that govern the audit, identifying deficiencies in the PBM’s methodology, and drafting an appropriate response that preserves the pharmacy’s rights under the applicable contract and applicable law.  Too often, pharmacies retain legal counsel after already submitting a response that inadvertently concedes key points.

Second-Half Outlook: Audits Will Continue and Standards Will Tighten

In light of recent trends observed in the first half of 2025, there is every indication that PBM audits will not only continue but expand in scope and intensity.  Pharmacies should expect narrower documentation standards and a greater likelihood of even minor discrepancies being treated as material breaches. 

The increasingly hostile environment requires a fundamental shift in how pharmacies manage compliance.  Documentation can no longer be treated as a formality.  Rather, it is the pharmacy’s first line of defense. Audit readiness is not just a legal issue; it is an operations issue.  The continuity of the pharmacy’s business could depend on its preparedness and response to a PBM audit.

Let Us Help

Our team has successfully defended retail and specialty pharmacies against a wide array of PBM audits and network actions.  We assist clients in developing internal compliance programs, conducting proactive reviews, and drafting strategic responses to audit findings that protect against recoupments and network loss.  Leveraging our legal knowledge and clinical understanding, we also represent pharmacies in appeals, arbitrations, and litigation stemming from audit disputes to push back when PBMs overreach.

If your pharmacy has received a notice of audit, is facing threat of termination, or wants to assess its risk exposure before an audit begins, we can help you navigate the process with confidence and clarity.  Now is the time to act – not after the audit is over, but before it begins.