In 2025, telehealth and online pharmacies are riding a wave of demand for compounded medications and controlled substances—semaglutide for weight loss, testosterone for TRT, buprenorphine for MAT—but behind the scenes, payment processing fees are eating margins alive. What looks like a standard 2.9% rate from Square or PayPal can balloon to 6–9% or more for compound and EPCS scripts, thanks to “high-risk” surcharges, reserves, and hidden add-ons from aggregators. For a platform processing $2M annually on these scripts, that’s $160K–$300K vanishing yearly—money that could fund more prescribers or marketing. The silent killer isn’t competition; it’s your processor. Here’s how these fees creep in, why compound and controlled scripts get hit hardest, and how to fight back without sacrificing growth.
Why Compound and Controlled Scripts Trigger Sky-High Fees
Compound pharmacies and EPCS platforms fall into the highest-risk tier for processors. Compounded drugs (custom GLP-1s like semaglutide/tirzepatide) and controlled substances (testosterone, Adderall, Suboxone) trigger red flags due to fraud potential, chargebacks from “buyer’s remorse,” and regulatory scrutiny from DEA and state boards. Aggregators—the go-to for rejected merchants—pile on surcharges:
- Base rate jumps from 2.9% to 4.5–6% for controlled scripts.
- Compounded meds add another 1–3% “pharmacy risk” fee.
- Reserves (10–20% held 6–12 months) tie up cash flow.
A $299 semaglutide script at 7.5% costs $22.43 in fees vs. $8.07 at 2.7%—$14.36 lost per sale. At 5,000 scripts/month, that’s $71,800 gone. In 2025, with semaglutide demand up 40% (per IQVIA) and DEA audits rising, these fees aren’t just annoying—they’re existential.
The Aggregator Trap: Short-Term Fix, Long-Term Pain
Rejected by PayPal, Square, or Stripe? Aggregators seem like a lifeline, pooling high-risk merchants under one account. But the hidden costs are brutal:
- Surcharges stacked on surcharges—6–9% total for compound/controlled.
- Rolling reserves—10–20% held 180–365 days, starving cash flow.
- Sudden closures—one bad actor in the pool freezes everyone.
A men’s health platform processing $1.8M yearly on testosterone paid $162K in fees at 9% + 15% reserve—$270K tied up. They thought it was “the cost of doing business.” It wasn’t.
Real Fee Comparison: The Numbers Don’t Lie
Here’s what the same $100,000 monthly volume looks like across processors (2025 averages):
| Processor Type | Effective Rate | Annual Fees on $1.2M | Reserves | Notes |
|---|---|---|---|---|
| Big-Box (Square/PayPal) | Banned | N/A | N/A | No approval for controlled/compounded |
| Aggregator | 6–9% | $72K–$108K | 10–20% | High surcharges + holdbacks |
| Standard High-Risk | 4–5.5% | $48K–$66K | 5–10% | Still expensive, caps common |
| Leap Payments | 1–2% | $12K–$24K | None | Locked rates, unlimited volume |
At Leap’s rates, that same platform saves $138K–$246K yearly—enough for 20 more prescribers or a six-figure ad budget.
Check Out Just A Few of The Companies That Trust & Use Leap Payments
The Hidden Chargeback Bomb
Controlled and compound scripts carry 3–5% chargeback rates—clients dispute “didn’t work” or “never received.” Aggregators charge $25–$50 per dispute + lose the sale. A 4% rate on $100K monthly = 40 chargebacks = $1,000–$2,000/month in penalties alone. Leap’s fraud tools and dispute support cut rates 40–60%, winning 70% of fights—real money back in your pocket.
Stop letting processors steal 8–15% of every script. Leap Payments delivers:
- 1–2% Locked Rates – Save $100K–$300K/year vs. aggregators
- No Reserves or Caps – Unlimited volume, no surprises
- Next-Day Funding – Cash for ads, doctors, inventory
- Free Equipment* – Terminals & gateways (*for qualifying merchants)
- Dedicated Support – We fight chargebacks so you don’t lose sales
One client dropped from 5.8% → 1.35% and saved $187K in year one—money that built their brand, not the processor’s.
Real-World Savings: From Bleeding to Booming
A telehealth pharmacy specializing in compounded semaglutide and testosterone was paying 5.8% + 15% reserve to an aggregator—$139K yearly in fees on $2M volume, plus $300K tied up. One state board inquiry triggered a 142-day freeze, costing $420K in lost sales. They switched to Leap: 1.35% locked rates, no reserves, next-day funding. Year 1 savings: $187K. They reinvested in X ads and a client portal, boosting revenue 45% to $2.9M. Same scripts, same doctors—just a processor that didn’t bleed them dry.
Leap Payments: Your 2025 Partner
The silent margin killer in compound and controlled scripts is your processor. Leap Payments turns it into your biggest advantage with 1–2% rates, no reserves, next-day funding, and free equipment for qualifying merchants. Visit LeapPayments.com or call (800) 993-6300 for same-day approval and a free savings audit. Your margins—and your growth—depend on the decision you make today.
Reclaim Your Margins
In 2025, every percentage point matters. Compound and controlled scripts don’t have to cost you 8–15% in hidden fees. Audit your processor, demand transparency, and switch to a partner that grows with you. Leap Payments is that partner—because your telehealth pharmacy deserves every dollar you earn.
Contact Us Below & Secure Your Lifetime Rate Lock Today!
Or Call: (800) 993-6300
