Bookkeeping and Tax for Independent
Medical and Healthcare Practices
Monthly bookkeeping, payroll, and tax services for physicians and healthcare practice owners across the country. A second-generation family firm based in Lenexa, Kansas.
Since 1995 • Tax Work by Enrolled Agents
Where We Can Help
Running a practice means running a business alongside patient care. These are the money problems we hear about most from practice owners.
Collections That Don't Add Up
Your billing system shows one number and your bank shows another. Each month we compare reported insurance collections against actual deposits, so gaps get caught while they can still be fixed.
Books Months Behind
When the books fall behind, it's hard to know where the practice stands. We bring them current first. Then we close them every month and send a one-page summary you can read in a few minutes.
Provider Pay by Spreadsheet
Working out provider or clinician pay by hand every pay period invites errors and disagreements. We calculate it from the terms of your existing compensation agreements, then run the payroll.
Filing Without a Plan
Practice owners tend to be high earners, and a return filed in April can't change much. Each year we plan ahead on business structure, owner pay, retirement contributions, and equipment purchases to help lower what you owe.
IRS and State Notices
A letter from the IRS or a state agency can be routine or serious, and it's hard to tell which. Our enrolled agents review it, respond on your behalf, and follow it through to the end.
Opening Your Own Practice
Leaving employment to open a practice means making a lot of financial decisions at once. We set up your business structure, books, payroll, and software before you see your first patient.
A Family Firm Since 1995
Founded by Melissa Baker, CPA, and now led by her daughter, Marcella Nichols. We are a family firm focused on independent healthcare practices nationwide.
Rooted in Lenexa
We have worked from Lenexa, Kansas for three decades and have been voted among the Best of Lenexa eight years in a row. Remote clients work with the same firm our local clients have relied on for years.
A Team That Knows You
Marcella spent seven years in recruiting and led a hiring team before taking over the firm. She hires credentialed enrolled agents who take the time to learn your practice. You won't be routed through a call center.
A Physician on Our Team
Marc Eastin, our Chief Information Officer, is a practicing neurosurgeon who also owns a business. He knows what it's like to be the client, and he designed our systems around that.
Clients Who Stay
Many of our client families have worked with us for two or three generations. Even clients who move out of the country keep working with us. We think that says more than anything we could write here.
Our Services
Our healthcare bookkeeping services are built around how practices actually bring in revenue and pay their people.
Monthly Bookkeeping
Your books are closed every month and summarized on one page you can read in a few minutes. If the books are behind, we bring them current first. For practices that bill insurance, we check that what your billing system says was collected actually reached the bank.
Payroll
Payroll for your front desk, clinical staff, and providers, run through Gusto and set up correctly in every state where your people work.
Tax Returns
Returns for the practice and its owner, quarterly estimates, and IRS or state notices handled by enrolled agents.
Tax Planning
A plan made each year to lower your tax bill. We look at how the practice is structured, how you are paid, your retirement contributions, and when to buy equipment.
Bill Pay
Vendor, rent, supply, and malpractice invoices paid on schedule. You approve each payment from your phone and we handle the rest.
New Practice Setup
Business structure, books, payroll, and software set up before your practice opens, so the financial side works from the first patient.
Advisory
Regular meetings about forecasts, hiring, and big purchases, built on your own books, so decisions about the future of your practice aren't based on guesswork.
Hiring & HR Support
Help finding, hiring, and onboarding staff for independent medical practices. Job descriptions, pay benchmarks, offer letters, onboarding paperwork, and an employee handbook, with a 90-day replacement guarantee.
Provider Pay Calculations
We calculate partner and provider pay each month from your production reports, following the compensation agreements you already have. The results go straight into payroll. Nobody has to do it by hand or argue over the math.
Clinician Pay
Session-based clinician pay calculated every pay run, following the practice's existing compensation agreements, so clinicians are paid correctly and on time.
Treatment Profitability
See what each treatment actually earns after product cost and commissions, and keep prepaid packages and memberships from inflating your revenue.
Multi-Entity Bookkeeping
Separate, accurate books for your practice, the building it operates in, or a med spa's management company and medical entity.
Sales Tax Filing
Sales tax on the skincare, supplements, and eyewear your practice sells is tracked and filed on time. We file in every state where you sell. The tax you collect from patients reaches the state correctly, and your books show how it got there.
Side-Income Package for Employed Physicians
Bookkeeping and tax for doctors with income outside their main job, such as locums, expert witness work, or medical directorships. Your side income is tracked, your quarterly estimates are calculated, and your return is prepared by enrolled agents.
Practices We Serve
We work exclusively with medical practices. We know how clinical revenue flows and how physician and staff compensation works across different practice models
Independent Physician & Surgical Practices
Medical & Healthcare
Physician-owned practices where insurance payments arrive late and adjusted, provider pay depends on production, and the owner is a high earner.
Behavioral Health Group Practices
Healthcare
You built a group practice one clinician at a time. Getting every clinician paid correctly shouldn't cost you your weekends.
Medical Spas & Aesthetic Clinics
Healthcare
We show you what each treatment earns after product and commissions, and keep package money from inflating your numbers.
Direct Care & Integrative Medicine
Healthcare
Most direct care and concierge doctors are running a business for the first time. We set up the books, track membership revenue, handle sales tax on retail products, and plan your taxes before they come due.
Dental Practices
Healthcare
Associate pay calculated from your own agreements, separate books for the building, and a yearly tax plan for owner dentists.
Therapy & Rehab Practices
Healthcare
Physical therapy, OT, speech, and chiropractic practices pay clinicians by productivity. We calculate that pay from your agreements and check collections against the bank.
Eye Care & Hearing Practices
Healthcare
Part medical practice, part retail store. We check insurance collections against deposits and track optical and hearing aid sales.
~1,000
Tax returns a year
48
States with clients
81%
Multi-generation clients
What Clients Say
Here is what a few of them have to say about working with Baker's.
"Baker's Bookkeeping and Tax Services is simply outstanding! Their professionalism and attention to detail are unmatched. They don't just file your taxes—they dive deep to maximize your savings and provide valuable recommendations for future planning. If you want top-notch tax assistance with a proactive edge, Baker's is the way to go!"
Daniel Welsh
A Family-Run Firm Since 1995
Let's Talk About
Your Practice
Tell us about your practice and where you could use some help.
