Medical practices & clinics
Books and taxes for medical billing companies.
Some clients pay a percentage of what you collect for them, others pay a flat monthly fee, and your billers are spread across a dozen states. 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 $23,600. One percentage-fee client had a strong collections month, so their invoice ran higher than usual, and I flagged it so you'd know why this month looked better.
- Client invoice, percentage feePercentage-of-collections revenue
- Client invoice, flat monthly feeFlat-fee client revenue
- Waystar clearinghouse subscriptionClearinghouse and software costs
- Remote biller payrollBilling staff wages
- Contract coder payoutContract coder pay
Why your books are different
A medical billing company's books go wrong across two different fee models.
Some clients pay you a percentage of what you collect for them, so your revenue rides on their performance, while others pay a flat fee no matter what. Add a remote workforce of billers and coders spread across states, and a generalist has no framework for keeping any of it straight.
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1
Percentage-fee revenue rides on client performance
When your fee is a percentage of what a client practice actually collects, a slow month for them is a slow month for you too, and it's easy to mistake a client's bad month for a problem in your own business.
What we doKeeps percentage-of-collections revenue tracked by client, so a dip tied to one client's slow month reads as exactly that, not as a business-wide problem. -
2
Flat-fee and percentage-fee clients get blended together
A flat monthly fee client pays the same every month regardless of volume, while a percentage-fee client's payment swings with their own business, and blended into one revenue number you lose the ability to see which model is actually more stable or more profitable for you.
What we doKeeps flat-fee and percentage-fee client revenue in separate lines, so you can compare how each model actually performs for your business. -
3
A remote, multi-state workforce complicates payroll
Billers and coders working from different states, some on payroll and some as contractors, creates real complexity that a generalist bookkeeper often misses until it becomes a bigger problem.
What we doKeeps billing staff wages and contract coder pay in clear, separate lines, and flags multi-state payroll questions for the accountant rather than guessing. -
4
Clearinghouse and software costs scale with client count
Clearinghouse access, claim scrubbing tools, and per-client software fees grow as you add clients, and if that cost isn't tracked against client revenue, you can't tell whether a new client is actually profitable once software costs are counted.
What we doKeeps clearinghouse and software costs in their own line, tracked against revenue, so client profitability is a real number.
Your categories
The categories Gus keeps for a medical billing company.
Set up once for how your different client fee models and your staff all get paid. You never pick a category. He does, and an accountant checks it.
Money in
- Percentage-of-collections revenueClient fees based on a share of what you collect for them, tracked by client.
- Flat-fee client revenueClients paying a fixed monthly amount regardless of volume.
- Onboarding and setup feesOne-time fees charged when a new client comes on board.
- Coding and consulting feesAny standalone coding review or consulting work billed apart from ongoing billing services.
Money out
- Billing staff wagesEmployed billers and coders, kept apart from contractor pay.
- Contract coder pay1099 coders and billers working on a contract basis.
- Clearinghouse and software costsClaim submission, scrubbing, and practice management integration tools.
- Training and certificationCoding certification courses and renewal fees for staff.
- Client acquisition costsSales commissions and marketing tied to bringing on new clients.
- Professional liability insuranceCoverage for billing and coding services provided to clients.
- Office and remote work costsEquipment and software supporting a distributed workforce.
What we watch for you
- Revenue by client
How much each client contributes, so one client's dip doesn't get mistaken for a company-wide problem.
- Fee model mix
How much revenue comes from percentage-fee clients versus flat-fee clients.
- Cost per client
What software, staffing, and clearinghouse costs run against each client's revenue.
- The set-aside
What you will owe, tracked every month, so April is a number you already knew.
Ask Gus
Things medical billing company 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 percentage-fee revenue by client, and this looks tied to that client's own slow month, not a problem on your end. Worth a call to check in with them, but the books look fine.
I keep the two revenue types in separate lines, so you can compare them directly instead of guessing from one blended total.
It can affect payroll and tax requirements by state. That's above my pay grade, so I flagged it for the accountant to review your setup.
The tax side
The tax side of a medical billing company.
Most of what matters here is worker classification for a remote, multi-state team and tracking revenue by client fee model.
What your return has to get right
Your accountant signs it, so it gets done right the first time.
- Employee or contractor for billers and codersA biller who works your set schedule and uses your systems is usually an employee, while one who sets their own hours and works for multiple billing companies may be a contractor. Getting this wrong across many staff members gets expensive fast.
- 1099-NEC for contract codersAnyone not on payroll who is paid $2,000 or more in 2026 gets a 1099-NEC by January 31.
- Multi-state payroll and nexusEmploying staff across several states can create tax filing obligations in each of those states, a detail that needs a closer look as your team grows.
- The pass-through deductionMost owners can take up to 20 percent of business profit off their taxable income. It comes out right when revenue by client and fee model is tracked clearly all year.
Deductions medical billing companies miss
Your bookkeeper knows what to look for in your statements. You never have to.
- Clearinghouse and software subscriptions
- Coding certification and training
- Contract coder payments
- Professional liability premiums
- Client acquisition and marketing costs
- Remote work equipment
- Continuing education for staff
- Business insurance
- Office and administrative software
- Travel for client onboarding
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 medical billing company year, kept every month.
Client fee cycles and staffing needs shift through the year. Your taxes run 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, any contract coder's 1099 is ready, 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 client mix or new hires changed the number.
- October
Before year end
Gus looks at anything worth doing before December, including whether your staffing costs are keeping pace with client growth.
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 medical billing companies. 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 medical billing company owners ask first.
Do you handle the actual billing and claims work for our clients?
No. Gus keeps your own company's books, the revenue you earn and the costs you carry running this business. The billing and coding work you do for your clients stays entirely yours.
How do you track clients on different fee structures?
Percentage-of-collections revenue and flat-fee revenue are kept in separate lines, tracked by client, so you can see how each client and each model is actually performing.
Our staff is spread across a lot of states. Does that complicate our taxes?
It can, since multi-state payroll sometimes creates filing obligations in each state. Gus flags that setup for the accountant to review rather than guessing.
Is it worth knowing how much a specific client costs us in software and staffing?
Many owners find it very useful. Gus tracks clearinghouse and staffing costs against client revenue, so client profitability is a real number.
We mix employed billers with contract coders. Does that matter for taxes?
Yes, worker classification matters, and getting it wrong across several people gets expensive. Gus flags the setup so the accountant can confirm each role is classified correctly.
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.
More in medical practices & clinics
We keep books for the business next door too.
- Compounding pharmacies
- Durable medical equipment (DME) suppliers
- Elective 3D/4D ultrasound studios
- Independent pharmacies
- Mobile nursing & concierge nurse services
- Mobile phlebotomy services
- Mobile x-ray & ultrasound services
- Occupational health & DOT physical clinics
- Orthotics & prosthetics providers
- Sleep clinics
- Wound care clinics
- Allergy clinics
- Audiology & hearing aid centers
- Concierge medicine practices
- Direct primary care (DPC) practices
- Independent eyewear boutiques
- Naturopathic doctors
- Occupational therapy practices
- Pediatric therapy clinics
- Podiatrists
- Speech therapy practices
- Sports medicine clinics
- Tattoo removal clinics
- Fertility clinics
- Functional medicine practices
- Independent urgent care clinics
- Optometrists
- Pain management clinics
- Private practice physical therapy
- Regenerative medicine clinics
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