Pharmacy profits have been on a steady decline for years—but that there aren’t plenty of opportunities to increase profit and stay competitive.

Most pharmacists aren’t in it for the money, but money still matters if you want to be around in, say, five, ten, or even twenty years. You have to keep the lights on, sign paychecks for employees, and (hopefully) save yourself a piece of the pie, too.

As most pharmacists are well aware, staying afloat takes real strategy. But you can’t create a strategy—in other words, you can’t know where you’re going—if you don’t know where you’ve been.

On the other hand, if you can track your history, you’ll see what’s working, what’s not, and where you can pivot.

Enter the world of financial KPIs. KPIs, or key performance indicators, are measurable metrics that show how your pharmacy is doing across different areas of your business.

In effect, they give you real-world knowledge, and knowledge is power.

At our Connect 2025 Conference, Apex Pharmacy Consulting’s Joe Williams and Benjamin Jolley gave us a rundown of the most important KPIs every pharmacy should be tracking (all of which can be configured in PioneerRx).

So, if you’re looking for new ways to take control of your pharmacy’s finances, start here:
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Med Sync Metrics

What does every successful pharmacy have in common? If you said a solid medication synchronization program, well, you’d be right.

While 80% of pharmacies already offer med sync, there’s always room to grow your program—and for the 20% who aren’t yet on board, it’s never too late to start.

A well-run med sync program improves efficiency, increases fill volume, and strengthens adherence across the patient base. Plus, on the financial side of things, it cuts back on excess inventory and, therefore, costs.

To keep your program running at full steam, you should be keeping up with a few med sync KPIs. Here are a few to start with:

1. Total patient enrollments: Tracks how many patients are currently in your sync program. Higher enrollment signals stronger program adoption.
2. New patient enrollments per day: Measures daily growth in your sync program. A steady increase means your team is actively signing up new patients (and is a quick win you should celebrate).
3. ‍% of Rx volume filled through sync: Calculates how much of your total volume is synced. The higher the percentage, the more efficient your workflow and the more time you have for clinical care.
4. Offers to sync made: Tracks how often sync is offered and acts as a great litmus test for patient outreach.
   Bonus trip: Track the outreach medium (phone call, email, SMS, etc.) for even more tailored input. If enrollments are on a decline, host a quick training session with your staff to ensure they're promoting the program.
5. Inbound phone call volume: Measures how many calls you’re getting on a day-to-day basis. Fewer calls often signal that patients are on autopilot, giving your staff room to breathe and your profits room to grow.

Inventory Management Metrics

Inventory is the biggest expense in your pharmacy, but it’s among the hardest to manage.

According to the 2023 NCPA Digest, inventory accounts for nearly 78% of total operating costs in an average independent pharmacy.

And as most pharmacists know all too well, inventory can be finicky. Too much of it ties up your cash. Too little puts you at risk of shortages. And poor ordering habits can increase your overall cost of goods.

There’s no perfect formula, but there are smart ways to keep things in check.

Some of the most helpful KPIs to look for include:

6. Inventory valuation: Shows the total dollar value of what’s on your shelves. An inflated number could mean cash is getting tied up in excess stock.
7. Inventory turnover rate: Measures how often inventory is sold and replaced. A higher rate = leaner inventory. The national average is 11 times a year, so anything lower is a red flag.
8. Key product inventory (multi-store): Helps you track essential items across all locations so you can redistribute stock and avoid over-ordering.

Profit and Reimbursement Metrics

Reimbursements are shrinking, but your overhead isn’t.

According to the NCPA Digest, gross profit margins dropped to 19.7% in 2024—the lowest point in the past decade.

Now more than ever, pharmacies are feeling the squeeze from below-cost third-party reimbursements, rising labor costs, and inflation across the board.

The message is clear: You can’t afford to guess where your profit is coming from. And you definitely can’t afford to let manual errors, outdated pricing, or poor payer contracts chip away at your margins.

These reports can help keep you in control:

9. Retail gross profit report: Breaks down profit from your front-end sales and shows you which OTCs are pulling their weight. From there, you can adjust marketing efforts to increase high-margin sales.
10. Basis of reimbursement summary: Shows how prescriptions are being reimbursed and helps you identify low-paying plans or problematic payers.
11. Price override audit: Shows manual price changes at the register, which can help catch errors or uncover training gaps among your staff.

Workflow Metrics

After inventory, your next biggest expense is your staff—and with labor shortages continuing to ripple through pharmacies around the country, you want to make those dollars count.

If your team isn’t working efficiently, your entire operation slows down. That means that service stalls and profits drop.

In terms of efficiency, a 2019 study estimates that pharmacies fill up to 300 scripts per day. But how evenly is that workload spread across your staff? Are some employees underperforming while others are overwhelmed?

Workflow KPIs can help you track what’s moving, who’s doing the work, and where bottlenecks are forming. Key reports to run include:

12. Daily summary: Gives a snapshot of your top 10 and bottom 10 prescriptions for the day. Useful for identifying trends or outliers.
13. Productivity reports: Tracks individual team member output so you can reward high performers and support those who are falling behind.
14. Transfer report: Monitors inbound and outbound transfers. Can reveal patient churn or opportunities for collaboration with other pharmacies. Remember: Not all outbound transfers are a bad thing!

Conclusion

It’s no secret: staying profitable in today’s industry is tougher than ever.

Margins are tighter, costs are climbing, and the pressure is on. But if there’s one thing independent pharmacies have always done well, it’s adapt.

The most successful don’t wait for things to go wrong. They keep a pulse on performance, spot issues early on, and shift course when they need to.

But to have that kind of agility, you first have to have visibility. You can’t fix what you don’t see, but KPIs keep important metrics in your field of vision.

The right KPIs give you a clear picture of what’s working, what’s not, and where to focus next. And when they’re built right into PioneerRx, they only take a few minutes to configure.

So, take some time to explore these reports. See what they’re telling you. And if something needs to change, you’ll be ready.

And if you want even more action-packed tips to maximize your pharmacy software, consider joining us next year at Connect 2026.