You spend 20 minutes with a patient, reviewing their “shoebox” of medications. You catch a duplicate therapy, you fix an adherence issue, and you explain exactly why they need to take their statin at night. The patient leaves happy and healthier.

But when you look at the bottom line for that interaction, the revenue is often… zero.

For decades, medication therapy management (MTM) was something we did out of the goodness of our hearts. It was “part of the job.” But in today’s pharmacy economy, where dispensing margins are disappearing, you can no longer afford to work for free.

MTM for pharmacists is one of the most potent tools we have to diversify revenue. But turning clinical care into a paid claim is not as simple as scanning a bottle.

I’ve seen many pharmacy owners launch an MTM pharmacy program with high hopes, only to get bogged down by rejections, audits, and low reimbursement. Why? Because billing pharmacy services on the medical side is a minefield if you don’t know where to step.

Here are the most common pitfalls in MTM billing and—more importantly—how to avoid them.

Pitfall #1: Relying 100% on MTM Platforms (The “Queue” Trap)

Most independent pharmacies start their MTM journey with platforms like Outcomes or Mirixa. These platforms are great entry points because they hand you the patients.

The Mistake: You only provide MTM services to the patients that pop up in your queue. The Reality: If you wait for a platform to tell you who to treat, you are leaving 80% of the revenue on the table. You have hundreds of patients walking through your door who need MTM but aren’t flagged by a Part D platform.

The Fix: You must move toward direct medical billing. This means identifying your own high-risk patients (private pay, state Medicaid, or Medicare Part B) and billing them directly using CPT codes. This puts you in control of your MTM outcomes and revenue, rather than waiting for a third party to send you work.

(Editor’s Note: Not sure how to find these patients? Read our guide: How to Launch MTM in Your Pharmacy: A 5-Step Guide for Owners.)

Pitfall #2: The “New” vs. “Established” Patient Coding Error

When you start billing medical claims directly (using a CMS-1500 form), you enter the world of CPT codes. The most common reason for an audit or denial is using the wrong code for the wrong patient.

The Mistake: consistently billing the higher-paying “New Patient” code for everyone.

The Fix: Know your definitions.

• 99605 (New Patient): Use this for the first 15 minutes of an MTM service provided to a patient you have never seen for MTM before (or haven’t seen in 3 years).
• 99606 (Established Patient): Use this for the first 15 minutes of an MTM service for a patient who has received MTM from you in the past 3 years.
• 99607 (Add-on): Use this for each additional 15 minutes.

Pro-Tip: Most of your patients are “Established” because they fill prescriptions with you. Be conservative. If you bill 99605 for a patient who has been filling with you for a decade, you are inviting an audit.

Pitfall #3: The “15-Minute” Rule (Undervaluing Your Time)

Pharmacists are humble. We often rush through a consult or under-report our time because we don’t want to “overcharge.”

The Mistake: You spend 25 minutes with a patient but only bill for the base 15 minutes (99606). The Reality: You are literally throwing money away.

The Fix: Medication therapy management is a time-based service.

• If you spend 1-15 minutes: Bill 99606.
• If you spend 16-30 minutes: Bill 99606 AND 99607.
• If you spend 31-45 minutes: Bill 99606 AND 99607 (x2 units).

Track your time religiously. If you did the work, bill for it.

Pitfall #4: The “If It Wasn’t Written Down…” (Documentation Failures)

In the PBM world, the “proof” is the signature on the log. In the medical billing world, the “proof” is the SOAP note.

The Mistake: You perform a great CMR (Comprehensive Medication Review), fix three problems, but your documentation is just a vague note saying “Patient counseled on adherence.” The Consequence: If you are audited, that claim will be clawed back. 100% of the time.

The Fix: Every billable MTM encounter requires a formal SOAP note:

• S (Subjective): What the patient told you (“I forget to take my evening pills”).
• O (Objective): What you observed (Blood pressure 140/90, Refill history shows gaps).
• A (Assessment): Your clinical judgment (Non-adherence due to complexity).
• P (Plan): What you did (Synced meds, educated patient, sent fax to MD).

Without the SOAP note, the service didn’t happen.

Pitfall #5: Billing for “Incidental” Counseling

This is a tricky gray area. You cannot bill MTM for the mandatory counseling required by OBRA ’90 (the standard “do you have any questions?” at pickup).

The Mistake: Billing a medical claim for a routine counseling session during a standard refill pickup.

The Fix: MTM’s must be distinct, separately identifiable services.

• Schedule it: The best way to prove this is separate is to schedule it as an appointment.
• Face-to-Face: While some telehealth is allowed, face-to-face is the gold standard for initial assessments.
• Identify a Problem: The service must be medically necessary. You are identifying a problem (or potential problem) in their therapy, not just handing them a bag.

Pitfall #6: Giving Up After the First Denial

Medical billing is different from pharmacy billing. When a drug claim rejects, you fix it in 30 seconds. When a medical claim rejects, it can take weeks to figure out why.

The Mistake: Treating a rejected claim as a “loss” and moving on. The Reality: A rejection is just a request for more information.

The Fix: You need a process for “Denial Management.”

• Did you miss a modifier? (Check our article on Common Billing Coding Mistakes).
• Is the diagnosis code (ICD-10) valid?
• Is the patient actually covered?

Don’t let administrative fatigue rob you of revenue.

You Don’t Have to Navigate This Alone

Avoiding these pitfalls requires a shift in mindset. You have to stop thinking like a dispenser and start thinking like a provider.

The potential for MTM outcomes—both for your patient’s health and your pharmacy’s bottom line—is massive. But the administrative burden of billing shouldn’t be the reason you stop providing care.

Whether you handle this in-house or partner with experts, mastering the billing process is the key to unlocking the future of your pharmacy.