Medical practices & clinics
Books and taxes for functional medicine practices.
Cash-pay visits with a superbill for the patient, specialty lab costs, supplement dispensary commissions, and multi-month programs. 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
September came in at $18,400. The Fullscript commission deposit landed this month, so I kept it apart from visit revenue since it's a different kind of income entirely.
- New patient comprehensive intakeCash-pay visit revenue
- Fullscript commission payoutSupplement dispensary income
- Genova DiagnosticsSpecialty lab costs
- 3-month program enrollmentProgram package fees
- Practice management softwareSoftware subscriptions
Why your books are different
A functional medicine practice's books go wrong around being out-of-network.
You are paid directly by the patient, hand them a superbill to submit on their own, order labs that cost real money before a diagnosis even happens, and get a commission when a patient fills their supplement order online. A generalist has no framework for any of that.
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1
Superbills confuse what actually gets paid
Patients pay you in full and get a superbill to submit to their own insurance for possible reimbursement, but that reimbursement goes to the patient, not you, and it's easy to mistakenly expect insurance money that will never land in your account.
What we doBooks only what patients actually pay you directly, since the superbill reimbursement is between the patient and their insurer, not a transaction in your books. -
2
Specialty lab costs are paid before any revenue is certain
A comprehensive stool panel or a hormone test from a specialty lab can cost hundreds of dollars, ordered and paid for before you know whether the patient will continue with a full program.
What we doKeeps specialty lab costs in their own line, tracked against visit and program revenue, so lab spend shows up as its own real cost. -
3
Supplement dispensary commissions are a different kind of income
A commission payout from an online dispensary such as Fullscript is a percentage of what patients bought on their own, not a service you delivered directly, and blended with visit revenue it hides how much of your income depends on supplement sales.
What we doKeeps dispensary commission income in its own line, apart from visit and program fees, so you can see exactly how much of the month it represents. -
4
Multi-month programs get spent before they're delivered
A patient enrolling in a 3-month or 6-month program pays a large amount up front, but the visits, labs, and follow-up happen over the full length of the program.
What we doKeeps prepaid program revenue visible as its own line, separate from single visits, so a big enrollment month doesn't overstate itself.
Your categories
The categories Gus keeps for a functional medicine practice.
Set up once for how visits, programs, labs, and supplements all get paid. You never pick a category. He does, and an accountant checks it.
Money in
- Cash-pay visit revenueWhat patients pay you directly, out of network, at the time of the visit.
- Program package feesMulti-month enrollment fees paid up front, kept apart from single visits.
- Supplement dispensary incomeCommission payouts from Fullscript or a similar online dispensary.
- Lab markup revenueAny amount collected from patients above the direct lab cost, if you mark up specialty labs.
Money out
- Specialty lab costsTests ordered through labs such as Genova Diagnostics or a similar specialty lab.
- Clinical wagesHealth coaches, nurses, and clinical support staff, kept apart from provider compensation.
- Software subscriptionsPractice management and patient portal tools.
- Continuing educationFunctional medicine certifications and specialty training.
- Malpractice insuranceAnnual or quarterly premiums for the practicing providers.
- Rent and utilitiesOffice space for consultations and visits.
- Marketing for new patientsContent, referrals, and advertising that drives new enrollments.
What we watch for you
- Dispensary commission share
How much of each month's income comes from supplement commissions versus visits and programs.
- Lab cost per patient
What specialty labs cost against what a patient's program brings in.
- Program revenue owed
How much prepaid program money still represents visits and labs not yet delivered.
- The set-aside
What you will owe, tracked every month, so April is a number you already knew.
Ask Gus
Things functional medicine practitioners 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.
Only what she pays you directly shows up. The superbill and any reimbursement from her insurer is between her and them, not something that lands in your account.
I keep that in its own line, so you can see the exact share every month instead of guessing whether it's a little or a lot.
It's a real cost either way, and I track it against program revenue so you can see whether that upfront lab spend is paying off over time.
The tax side
The tax side of a functional medicine practice.
Most of what matters here is keeping dispensary commissions and lab costs separate, and knowing where the pass-through deduction starts to phase out.
What your return has to get right
Your accountant signs it, so it gets done right the first time.
- The pass-through deduction phases outA functional medicine practice can lose part or all of the 20 percent pass-through deduction once taxable income passes $201,750 single or $403,500 joint, since medical practices are a specified service trade.
- Dispensary commission incomeCommission payouts from a supplement dispensary are ordinary business income, reported the same as visit revenue, just tracked separately so the source stays clear.
- Specialty lab costsLab costs paid on behalf of a patient are generally deductible as an ordinary business expense, and any amount marked up and collected from the patient is reported as income.
- Contract health coachesA health coach who works independently, sets their own hours, 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 functional medicine practices miss
Your bookkeeper knows what to look for in your statements. You never have to.
- Specialty lab costs
- Continuing education and certifications
- Malpractice premiums
- Practice management software
- Patient education materials
- License renewal fees
- Content and marketing costs
- Office supplies for consultations
- Professional membership dues
- Referral program costs
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 functional medicine year, kept every month.
Programs, labs, and dispensary commissions each move on their own rhythm. Your taxes come on a fixed schedule. Your team keeps you ahead of both. 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 programs still running from prior months.
- 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 program enrollments or dispensary income changed the number.
- October
Before year end
Gus looks at anything worth doing before December, while many patients start planning a new program for the new 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 functional medicine practices. 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 functional medicine practitioners ask first.
Do you handle insurance billing or superbill submissions?
No. Gus does not handle insurance billing, medical coding, or claims of any kind, including submitting or tracking superbills. He books what patients pay you directly, since any insurance reimbursement goes to the patient, not your practice.
How does the Fullscript commission income actually get reported?
As ordinary business income, kept in its own line so you can see how much of your month comes from dispensary commissions versus visits and programs.
We front the cost of expensive specialty labs before some patients commit to a program. Is that risky for the books?
It's a real cost that Gus tracks against program revenue, so you can see whether upfront lab spend is paying off. Whether to change that policy is a business call for you.
Do I owe tax on supplement commissions the same way as visit income?
Yes, it's ordinary business income either way. Gus just keeps it labeled separately so the source is always clear on the books.
A patient enrolled in a 6-month program but stopped after two months. What happens to the rest of that revenue?
Gus keeps program revenue tracked separately from earned revenue as it's delivered. What to do about an incomplete program is a policy question for you and your accountant.
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