Medical practices & clinics
Books and taxes for compounding pharmacies.
Raw ingredients bought by the batch, PBM reimbursements that often pay less than the compound costs to make, and cash-pay scripts filling the gap. Gus sorts all of it, an accountant checks every transaction, and you get one number a month.
- From $197 a month
- An accountant on every transaction
- Cancel whenever
April came in at $25,900. Several PBM claims paid less than the compound cost to make, so I tracked those against ingredient cost to show where cash-pay pricing is actually needed.
- PBM reimbursement batchPBM reimbursements
- Cash-pay compound scriptsCash-pay revenue
- Active ingredient bulk orderRaw ingredient costs
- Sterile compounding hood servicingClean room equipment costs
- Pharmacist and technician payrollPharmacy wages
Why your books are different
A compounding pharmacy's books go wrong where ingredient cost meets PBM reimbursement.
You're buying raw ingredients by the batch, making a specific preparation for a specific patient, and often getting reimbursed by a pharmacy benefit manager at a rate that doesn't cover what the compound cost to make. A generalist has no framework for any of that mismatch.
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1
PBM reimbursements can pay less than the compound costs
A pharmacy benefit manager sometimes reimburses a compounded preparation at a rate below what the raw ingredients and labor actually cost, a losing transaction if it isn't tracked and caught early.
What we doTracks PBM reimbursements against ingredient cost by preparation type, so a losing reimbursement rate shows up as a number instead of getting lost in the total. -
2
Raw ingredient costs swing by batch and by supplier
Active pharmaceutical ingredients are bought in bulk and their price can shift meaningfully from one order to the next, and a single large ingredient order can be one of the largest expenses of the month.
What we doKeeps raw ingredient costs in their own line, tracked against compound revenue, so a price swing reads as a real cost shift, not a mystery. -
3
Cash-pay and PBM scripts get blended together
A compound rejected or underpaid by a PBM often gets converted to a cash-pay price for the patient, and blended with regular PBM-reimbursed scripts, you cannot tell how much of your revenue actually depends on cash-pay pricing.
What we doKeeps cash-pay revenue apart from PBM reimbursements, so you can see how much the pharmacy relies on each. -
4
Clean room and sterile compounding equipment reads as a supply run
Laminar flow hoods and sterile compounding equipment can cost tens of thousands of dollars, and filed as supplies, a purchase wrecks the month it was bought and hides what it's worth over years.
What we doFlags a big equipment purchase the day it lands, logs it as equipment, and lets the accountant decide how it gets written off.
Your categories
The categories Gus keeps for a compounding pharmacy.
Set up once for how scripts, ingredients, and equipment all get paid. You never pick a category. He does, and an accountant checks it.
Money in
- PBM reimbursementsDeposits from pharmacy benefit managers for compounded preparations.
- Cash-pay revenueScripts paid directly, often when PBM reimbursement is rejected or too low.
- Veterinary compounding revenuePreparations made for veterinary practices, kept apart from human scripts.
- Physician office dispensingBulk or office-use preparations sold directly to prescribing practices.
Money out
- Raw ingredient costsActive pharmaceutical ingredients and bulk chemicals used in preparations.
- Clean room equipment costsLaminar flow hoods and sterile compounding equipment, logged so they get written off right.
- Pharmacy wagesPharmacists and compounding technicians.
- Packaging and labeling suppliesVials, bases, and labeling materials for finished preparations.
- Facility costsRent and utilities for compounding lab space.
- Professional liability insuranceCoverage for the pharmacy and its pharmacists.
- Pharmacy management softwarePrescription tracking and billing tools.
What we watch for you
- PBM margin by preparation
What each compound type reimburses against what the ingredients cost to make it.
- Cash-pay share
How much revenue comes from cash-pay scripts versus PBM reimbursement.
- Ingredient cost trend
How raw ingredient prices are shifting month to month for your most-used compounds.
- The set-aside
What you will owe, tracked every month, so April is a number you already knew.
Ask Gus
Things compounding pharmacy owners ask Gus.
Text him like you would text anybody. He answers in plain English, and when a question is above his pay grade, an accountant looks and gets back to you.
I track PBM reimbursements against ingredient cost by preparation type, so if a rate isn't covering your cost, that shows up as a real number instead of hiding in the total.
I keep ingredient costs in their own line against compound revenue, so you can watch whether this is a one-time supplier price change or an ongoing shift.
I keep those in separate lines, so you can see that split directly instead of guessing from the total.
The tax side
The tax side of a compounding pharmacy.
Most of what matters here is tracking ingredient inventory correctly and knowing what qualifies as equipment versus supplies.
What your return has to get right
Your accountant signs it, so it gets done right the first time.
- Raw ingredient cost of goods soldActive pharmaceutical ingredients and bulk chemicals held for compounding are generally tracked as inventory, with their cost recognized as preparations are made and sold.
- Clean room and compounding equipmentLaminar flow hoods and sterile compounding equipment can usually be written off the year you buy them, with 100 percent bonus depreciation available for property acquired after January 19, 2025.
- The pass-through deduction phases outA compounding pharmacy providing personalized pharmacy services can lose part or all of the 20 percent pass-through deduction once taxable income passes $201,750 single or $403,500 joint, since some pharmacy services are treated as a specified service trade. This depends on how your practice is structured, so it's worth confirming with your accountant.
- Contract or relief pharmacistsA pharmacist covering occasional shifts who sets their own terms and bills you directly is often a contractor and gets a 1099-NEC if you pay them $2,000 or more in 2026, due January 31.
Deductions compounding pharmacies miss
Your bookkeeper knows what to look for in your statements. You never have to.
- Raw ingredient inventory
- Clean room equipment maintenance
- Packaging and labeling supplies
- Professional liability premiums
- Pharmacy management software
- License and registration renewal
- Continuing education for pharmacists
- Facility cleaning and sterility supplies
- Marketing to prescribing practices
- Shipping for compounded preparations
General information about 2026 federal rules, not advice for your business. Your accountant looks at your actual numbers before anything gets filed.
All year, not just April
A compounding pharmacy year, kept every month.
Ingredient costs, PBM reimbursement rates, and cash-pay demand each shift on their own schedule. Your taxes run on a fixed one. Your team keeps you ahead of all three. Every month in between, your bookkeeper closes the books and speaks up the moment something looks off.
- January
Plan the year
Last year's return gets started, and you get a monthly set-aside so April is already handled.
- April
Filed. Done.
Your return is filed and signed. No surprise bill, because the set-aside has been running since January.
- July
Halfway check
Where you stand, what you will owe, and whether ingredient costs or PBM rates changed the number.
- October
Before year end
Gus looks at equipment worth buying and anything worth doing before December, while checking whether ingredient pricing shifted much this year.
What you get
What you pay depends on what your business needs, and it does not move after that, busy season or slow. No hourly bills, no surprise invoices, no setup fee.
Book a call- Monthly bookkeeping
Every transaction sorted into categories set up for compounding pharmacies. You never categorize a thing.
- An accountant checks every transaction
Real review, every month, before your books close. Not a spot check.
- Your business tax return, filed
Prepared, reviewed, and signed by that same accountant every year.
- The monthly number
What you made, what you spent, what to set aside for taxes.
- Your own bookkeeper
A real person assigned to your business, in the app whenever you need them. No hold music.
- On your books all year
Every month, not just in April. Your team speaks up whenever something is worth your attention.
- Cancel any time
No contract. No cancellation call. Your books are yours.
Straight answers
Questions compounding pharmacy owners ask first.
Do you handle PBM billing or claims submission?
No. Gus does not handle insurance or PBM billing, claims, or reimbursement disputes. Your pharmacy software still handles that. Gus works from what actually lands in your bank account.
Can Gus tell us if a compound is losing money on PBM reimbursement?
Yes, he tracks PBM reimbursements against ingredient cost by preparation type, so a losing rate shows up as a real number you can act on.
Our ingredient costs vary a lot by supplier and batch. Can that be tracked?
Yes, raw ingredient costs are kept in their own line against compound revenue, so price swings read as real cost shifts instead of a mystery.
We do both human and veterinary compounding. Does that need separate categories?
Yes, and Gus already keeps veterinary compounding revenue apart from human prescriptions, so each side of the business is visible on its own.
How do you separate cash-pay scripts from PBM-reimbursed ones?
By the source of the deposit. Cash-pay revenue and PBM reimbursements are kept in separate lines from the start, so you can see how much the pharmacy relies on each.
Is a real accountant checking my books?
Yes. You get your own bookkeeper, Gus does the first pass on every transaction, and an accountant checks every one before your month closes. That same accountant prepares, signs, and files your business return. Goatkeeper is not a CPA firm, and we never pretend a person looked when they did not.
What does it cost, and can I cancel?
It starts at $197 a month, depending on what your business needs. No setup fee, no hourly bills, no contract. Cancel any time from the app, and your books go with you.
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What makes a bookkeeper worth paying for Every business we keep books for
Book a call
Pick a time. That's the whole signup.
Fifteen minutes with a real person on our team. They look at where your books are, tell you straight what it takes to get caught up, and get you set up on the spot if it fits.
- $197 a month to start
- An accountant on every transaction
- Cancel whenever