Medical practices & clinics
Books and taxes for independent pharmacies.
PBM reimbursements that get clawed back months later, a front-end aisle of retail products, and flu shots billed as their own service. 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
November came in at $22,400. A round of DIR fee clawbacks landed for prescriptions filled back in the summer, so I tied that reduction to the original claims instead of just calling it a cost.
- PBM reimbursement batchPrescription reimbursements
- DIR fee clawbackPBM fee clawbacks
- Front-end retail salesFront-end retail revenue
- Flu shot administration feesImmunization revenue
- Cardinal Health drug orderPrescription drug inventory
Why your books are different
An independent pharmacy's books go wrong months after the sale, not the day of it.
A prescription can look profitable the day it's filled and then get clawed back by the PBM months later, while a front-end aisle of snacks and greeting cards runs on a completely different margin than the pharmacy counter. A generalist books it all the day cash moves and misses both problems.
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1
DIR fees claw back revenue months after the fact
A pharmacy benefit manager can reduce what it pays for a prescription filled months earlier through a direct and indirect remuneration fee, which means a claim that looked fine in July can quietly shrink in November.
What we doTies DIR fee clawbacks back to the original claims they came from, so a delayed reduction reads as what it is instead of an unexplained cost. -
2
Front-end retail runs on different margin than prescriptions
Snacks, greeting cards, and over-the-counter products sold up front carry ordinary retail margin, nothing like the regulated, thin margin on a filled prescription, and blended together neither number makes sense.
What we doKeeps front-end retail revenue and its inventory cost apart from prescription revenue, so each side of the store shows its real margin. -
3
Immunization fees blend into prescription revenue
A flu shot or other immunization administered at the pharmacy counter bills as its own service, separate from filling a prescription, and lumped together you cannot tell how much of the month came from vaccine administration.
What we doKeeps immunization administration fees in their own line, apart from prescription dispensing revenue. -
4
Generic and brand margin get averaged together
A generic fill and a brand-name fill can carry very different reimbursement and cost, and averaging them together hides which mix is actually keeping the pharmacy profitable.
What we doTracks prescription revenue against drug inventory cost so shifts in generic versus brand mix show up as a real margin change.
Your categories
The categories Gus keeps for an independent pharmacy.
Set up once for how prescriptions, retail, and immunizations all get paid. You never pick a category. He does, and an accountant checks it.
Money in
- Prescription reimbursementsPBM and insurance deposits for filled prescriptions.
- Cash-pay prescription revenuePrescriptions paid directly without insurance or a PBM.
- Front-end retail revenueOver-the-counter products, snacks, and general merchandise.
- Immunization revenueFlu shots and other vaccines billed as their own service.
Money out
- Prescription drug inventoryBrand and generic medications purchased from wholesalers such as Cardinal Health or McKesson.
- Front-end retail inventoryOver-the-counter products, cards, and general merchandise stock.
- PBM fee clawbacksDIR fees and similar retroactive reductions tied back to original claims.
- Pharmacy wagesPharmacists and pharmacy technicians.
- Front-end retail wagesCashiers and stock staff, kept apart from pharmacy wages.
- Professional liability insuranceCoverage for the pharmacy and its pharmacists.
- Pharmacy management softwarePrescription processing, billing, and inventory tools.
What we watch for you
- DIR fee impact
How much revenue is being clawed back after the fact, tied to the claims it affects.
- Front-end retail margin
What retail products bring in against their cost, kept apart from prescription margin.
- Generic versus brand mix
How the split between generic and brand fills is shifting prescription margin.
- The set-aside
What you will owe, tracked every month, so April is a number you already knew.
Ask Gus
Things independent 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.
Unfortunately, yes, that's normal for PBM contracts. I tie clawbacks back to the original claims they affect, so it reads as what it is instead of a random cost hit.
I keep retail revenue and its cost apart from prescription margin, so you can see the real number for the front end on its own.
I keep immunization revenue in its own line, so you can see exactly how much vaccine administration added apart from regular prescription fills.
The tax side
The tax side of an independent pharmacy.
Most of what matters here is tracking drug inventory correctly and handling DIR fee timing.
What your return has to get right
Your accountant signs it, so it gets done right the first time.
- Prescription drug inventoryBrand and generic medications held for dispensing are generally tracked as inventory, with their cost recognized as prescriptions are filled rather than when purchased from the wholesaler.
- DIR fee and clawback timingA retroactive PBM fee reduces the income originally reported for the affected claim, which is why keeping clawbacks tied to the original transaction matters for an accurate return.
- Front-end retail inventoryOver-the-counter products and general merchandise are tracked as their own inventory, separate from prescription drugs, since their cost and margin behave differently.
- Immunization administration equipmentRefrigeration units and administration supplies for vaccines are generally deductible as ordinary business expenses in the year they're purchased or used.
Deductions independent pharmacies miss
Your bookkeeper knows what to look for in your statements. You never have to.
- Prescription drug inventory
- Front-end retail inventory
- Professional liability premiums
- Pharmacy management software
- Immunization supplies and refrigeration
- License and registration renewal
- Continuing education for pharmacists
- Point of sale equipment
- Marketing and community outreach
- Delivery costs for prescriptions
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
An independent pharmacy year, kept every month.
Flu season, front-end retail cycles, and DIR fee clawbacks each land 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, even with DIR fees still settling from last year.
- 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 DIR fees or front-end retail sales changed the number.
- October
Before flu season
Gus looks at anything worth doing before December, right as flu shot season brings its own wave of immunization revenue.
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 independent 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 independent pharmacy owners ask first.
Do you handle PBM billing or dispute DIR fees?
No. Gus does not handle PBM billing, claims, or fee disputes. He works from what actually lands in your bank account, and ties any clawback back to the original claim so the numbers stay honest.
Why do our numbers from a few months ago sometimes change?
That's usually a DIR fee clawback, common with PBM contracts. Gus ties it back to the original claim so it's clear what happened rather than looking like an error.
How do you separate front-end retail from prescription revenue?
By category from the start. Front-end retail sales and their inventory cost are kept apart from prescription revenue, so each side of the store shows its real margin.
Does flu shot revenue need its own tracking?
Yes, and Gus already keeps immunization revenue in its own line, apart from prescription dispensing, so you can see how much vaccine administration adds to the month.
Is it worth tracking our generic versus brand mix?
Many owners find it useful. Gus tracks prescription revenue against drug inventory cost, so a shift in that mix shows up as a real margin change.
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