Bookkeeping, payroll, and tax for independent healthcare practices, from a Kansas City firm trusted since 1995.

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New Practice Setup

Business structure, books, payroll, and software set up before your practice opens, so the financial side works from the first patient.

What This Is

Most doctors who open their own practice have spent their whole career as employees. The hospital or group handled payroll, taxes, and the books, and a paycheck showed up every two weeks with withholding already taken out. Opening a direct primary care, concierge, or integrative medicine practice changes all of that at once. The same is true for nurses and entrepreneurs opening a med spa for the first time.

New Practice Setup puts the financial side of the business in place before you see your first patient. That means the business structure and tax election, the bank accounts, the books in QuickBooks Online, payroll in Gusto, and the connections between your practice software, payment processor, and accounting system. Everything is built for how your practice actually earns money, whether that is monthly memberships, cash-pay visits, treatment packages, or retail products.

What Gets Set Up

Entity type and tax election, with help deciding whether and when an S-corp election makes sense. Business bank accounts and a clean break from personal spending. A QuickBooks Online chart of accounts designed for a medical practice. Gusto payroll for you and your staff. Sales tax registration if you sell supplements or skincare. A plan for owner pay and quarterly tax estimates.

Timing and Cost

The best time to start is 60 to 90 days before opening, though we can also help if you have already opened and things feel messy. A solo direct primary care practice needs less than a med spa with a management company and a separate medical entity. That is why pricing ranges from $500 to $5,000. You get a fixed quote before any work begins.

Why This Matters

Decisions made in the first few months tend to stick. An entity set up the wrong way, personal and business expenses mixed in one account, or startup costs that were never recorded can take a long time and real money to sort out later. Many new owners only find these problems at tax time, when the options for fixing them are limited.

There is also the adjustment from employee to owner. Nobody withholds taxes from your practice income, so the first tax bill often arrives larger than expected. Membership fees and prepaid packages bring in cash before the care is delivered, which can make the practice look more profitable than it is. Our Chief Information Officer, Marc Eastin, is a practicing neurosurgeon who also owns a business, so we have seen this transition from the physician’s side, not just the accountant’s.

The First Year Tax Surprise

Leaving employment means leaving automatic withholding behind. Without a plan for quarterly estimates and owner pay, new practice owners often face a large balance due plus underpayment penalties the following spring. That bill tends to land right when cash is tight and the practice is still growing.

Structure That Fits the Practice

Many states limit who can own a medical practice, which is why med spas are often split into a management company and a physician-owned medical entity. Getting the books and tax filings right for each entity matters from the start. We set up the financial side and work alongside your healthcare attorney on the legal requirements in your state.

What Changes

You open with a financial system that is already working. Payments from your practice software land in the right accounts. Your first payroll runs correctly for you and your staff. Expenses are categorized from day one, so you can see what the practice costs to run and how close you are to breaking even.

You also know what to expect. You know how much to set aside for taxes, when estimates are due, and how you will pay yourself. When setup is finished, the practice is ready for monthly bookkeeping and ongoing tax work without any cleanup in between. Your time can go to patients and building the practice instead of figuring out accounting software at night.

Clean Books From the Start

Every dollar is tracked properly from the first month, including startup costs spent before opening. Membership and package revenue is recorded in a way that reflects care actually delivered. When you need numbers for a lender, a lease, or your own planning, they are accurate and ready.

A Clear Plan for Year One

You leave setup with a written plan covering owner pay, quarterly tax estimates, and the key deadlines for your first year. An enrolled agent reviews your situation and answers your questions along the way. Nothing about your first tax season should come as a surprise.

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Baker's Bookkeeping & Tax Services has handled bookkeeping, payroll, and tax work from Lenexa, Kansas, since 1995. Today we serve independent medical and healthcare practices nationwide, with tax work and IRS notices handled by credentialed enrolled agents. We prepare around 1,000 returns a year, and most of our clients are families who have trusted us for two or three generations.

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