Bookkeeping and Tax for San Antonio Medical Practices
Bookkeeping, payroll, and tax for San Antonio medical practices. Built for direct primary care, independent physicians, and doctors leaving military or hospital employment.
Bookkeeping and Tax for San Antonio Practices
San Antonio has become one of the most active cities in Texas for direct primary care. Physicians here are leaving hospital systems and military medicine to open membership practices, and many of them are running a business for the first time. Add a large base of independent specialists and a steady flow of TRICARE patients, and you get a city full of practices that need books built around healthcare.
Baker’s Bookkeeping & Tax Services has kept books and prepared taxes since 1995 from our office in Lenexa, Kansas. Our remote team now works with practice owners across the country, including here in Bexar County. Your books, payroll, and returns are handled by enrolled agents who take the time to learn how your practice runs. You won’t be passed around a call center.
Monthly Bookkeeping
Monthly Bookkeeping
Books closed every month in QuickBooks Online, with a one-page summary you can read in a few minutes. For practices billing TRICARE, Medicare, and commercial plans, we check that what your billing system says was collected actually reached the bank. If your books are behind, we bring them current first.
Tax Planning
Tax Planning
Texas doesn’t tax your personal income, so the federal return is where almost all of your tax bill lives. That makes entity structure, a reasonable owner salary, retirement contributions, and the timing of equipment purchases worth real money. We build a plan each year and review it well before December.
Tax Returns and Texas Filings
Tax Returns and Texas Filings
Returns for the practice and for you personally, along with quarterly estimates. We also keep track of the annual Texas franchise tax filing that most practice entities still owe the Comptroller. If an IRS or state notice shows up, our enrolled agents handle it.
Payroll
Payroll
Front desk staff, nurses, medical assistants, and providers paid on time through Gusto. When PCS orders move a military spouse on your team to another state, they can keep working for you remotely. We run payroll in any state without switching systems.
San Antonio Practices We Work With
Healthcare is one of San Antonio’s biggest industries. The South Texas Medical Center anchors the northwest side. Brooke Army Medical Center and the rest of Joint Base San Antonio bring physicians and military families in from all over the country. New practices keep opening out toward Stone Oak, Alamo Ranch, and Schertz.
Many owners we talk to here trained or served in military medicine, finished their commitment, and decided to stay. Others left a hospital job to practice on their own terms. If that’s where you are, our new practice setup work gets your entity, books, payroll, and software ready before the first patient walks in. Marc Eastin, our Chief Information Officer, is a practicing neurosurgeon and business owner, so we understand that move from the inside.
Direct Primary Care and Concierge
Direct Primary Care and Concierge
Membership practices run on monthly fees instead of insurance claims. We keep membership income separate from in-office dispensing and lab revenue, file sales tax on supplements and retail products where it applies, and plan taxes around a business model that’s new to most owners.
Independent Physicians and Specialists
Independent Physicians and Specialists
Primary care, pediatrics, surgical specialties, dermatology, and pain management practices around the Medical Center and beyond. Our medical practice bookkeeping and tax services include collections matched to deposits, provider pay calculated from your existing compensation agreements, and separate books when your building sits in its own entity.
Behavioral Health Groups
Behavioral Health Groups
San Antonio’s large veteran and military family population keeps therapists, psychologists, and psychiatrists busy. Paying clinicians correctly under session-based agreements is usually the hardest money problem for these groups. We calculate clinician pay every pay run from the agreements you already have in place.
Med Spas and Aesthetic Clinics
Med Spas and Aesthetic Clinics
Alamo Heights, Stone Oak, and The Rim all have their share of med spas. Texas corporate practice of medicine rules lead many owners to split into a management company and a physician-owned medical entity. We keep separate books for each, track prepaid packages so revenue isn’t overstated, and file sales tax on retail skincare.
Common Questions About This Area
Do you work with practices across San Antonio?
Yes. We work with practices in the Medical Center, Stone Oak, Alamo Heights, Alamo Ranch, Schertz, Boerne, New Braunfels, and the rest of the metro. Our office is in Lenexa, Kansas, and all of our work is done remotely, so your location doesn't change the service you get.
Texas has no state income tax. Do I still need tax planning?
Yes, and it may matter more. With no state income tax, nearly your entire tax bill is federal. Choices about entity structure, owner salary, retirement contributions, and equipment timing all land on that one return. Most practice entities also still have an annual Texas franchise tax filing, even when nothing is owed.
I'm leaving military medicine to open a direct primary care practice. When should I call?
Before you open, if you can. Our New Practice Setup service puts your business structure, books, payroll, and software in place before your first patient. It's a one-time fee between $500 and $5,000 depending on how much needs to be built.
What does monthly bookkeeping cost?
Between $500 and $1,500 per month depending on the size and complexity of your practice. If your books are behind when we start, catch-up work is billed at 75% of the monthly fee for each month we bring current.
We bill TRICARE, Medicare, and commercial plans. Can you check our collections?
Yes. Each month we compare what your billing system reports as collected against the deposits that actually reached your bank account. Gaps between the two are common in medical practices, and they're much easier to fix when someone catches them early.
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