Bookkeeping and Tax for Chicago Medical Practices
Bookkeeping, payroll, and tax for Chicago physician practices, med spas, concierge doctors, dental offices, and behavioral health groups.
Bookkeeping and Tax for Chicago Practices
Chicago has no shortage of accounting firms. Many are built for hospital systems and large groups, and others take any small business that walks in the door. Independent practices often end up somewhere in between, with a firm too big to give them real attention or one that doesn’t understand why insurance deposits never match the billing report. Our remote division focuses on independent healthcare practices and the people who own them.
Baker’s Bookkeeping & Tax Services started in Lenexa, Kansas in 1995 and prepares around 1,000 tax returns a year. Today we serve Chicago practices remotely using QuickBooks Online and Gusto. Your work is handled by a team of enrolled agents who learn how your practice actually runs. Our CIO, Marc Eastin, is a practicing neurosurgeon who also owns a business, so we know what a doctor’s week looks like and how little of it is left for paperwork.
Monthly Bookkeeping
Monthly Bookkeeping
Books closed every month with a one-page summary you can read in a few minutes. For practices billing Blue Cross Blue Shield of Illinois, Medicare, and other payers, we check that what your billing system reports as collected actually reached the bank. If your books are behind, we bring them current first.
Payroll Across State Lines
Payroll Across State Lines
Plenty of Chicago practices have staff who live in Northwest Indiana or southern Wisconsin, or providers who work remotely. We run staff and provider payroll through Gusto in any state, and we account for the reciprocal agreements Illinois has with its neighbors so withholding is handled correctly for each employee.
Tax Returns and Planning
Tax Returns and Planning
We provide tax services for physicians and other practice owners, covering the practice return, your personal return, and quarterly estimates. Enrolled agents handle any IRS or Illinois Department of Revenue notices. Each year we also review structure, owner salary, retirement contributions, and equipment timing, including how the Illinois replacement tax on S corporations and partnerships affects the numbers.
Chicago Sales Tax
Chicago Sales Tax
Retail skincare, supplements, and eyewear sold in Chicago carry a combined sales tax rate above 10 percent, one of the highest of any large city in the country. We file on time and keep product sales separate from service revenue so you aren’t collecting or remitting the wrong amount.
Chicago Practices We Work With
Chicago is one of the ten largest med spa markets in the country and one of the top three cities for concierge doctors. Add a deep base of independent physicians, dentists, and therapists across the city and suburbs, and you get a lot of practice owners who spent years training in medicine and very little time learning to run a business.
Many of the doctors we talk with recently left a hospital system or large group to go out on their own. The move toward concierge and direct care medicine has been especially strong here, from offices in the Gold Coast and Lincoln Park to the North Shore suburbs. Whatever the model, the needs are similar. Clean books, payroll that runs on time, and a tax plan built before December instead of after April.
Med Spas and Aesthetic Clinics
Med Spas and Aesthetic Clinics
River North, the West Loop, and the Gold Coast are full of med spas, laser clinics, and cosmetic dermatology offices. Our treatment profitability reports show what each injectable or laser service earns after product cost and commissions, with prepaid packages and memberships tracked so revenue isn’t overstated. When a med spa runs a management company alongside a physician-owned medical entity, we keep separate books for each.
Concierge and Direct Care
Concierge and Direct Care
Membership practices bring steadier revenue but a new set of questions for doctors running a business for the first time. We set up the entity, books, and payroll before you open, then keep monthly records that show how membership growth compares to your costs. Supplements and retail products are tracked separately for sales tax.
Physician and Dental Practices
Physician and Dental Practices
Primary care, surgical specialties, dermatology, general dentistry, and orthodontics. We calculate partner, provider, and associate dentist pay each month from production numbers, following the compensation agreements you already have. Practices that own their building get separate books for the real estate entity.
Behavioral Health Groups
Behavioral Health Groups
Therapy and counseling groups in Lakeview, Andersonville, Evanston, and Oak Park often pay clinicians per session, and getting that right every pay run is the hardest part of the business. Our President, Marcella Nichols, holds a master’s in clinical psychology and spent seven years in recruiting and HR. We calculate clinician pay from your existing agreements and help when it’s time to hire.
Common Questions About This Area
You're based in Kansas. How does that work for a Chicago practice?
Everything runs remotely through QuickBooks Online, Gusto, and a secure document portal. We're on Central time just like Chicago, so calls and deadlines line up. Most practice owners prefer working this way because there's nothing to schedule around clinic hours.
What does monthly bookkeeping cost?
Monthly bookkeeping runs $500 to $1,500 depending on transaction volume and the size of your practice. If your books are behind, each catch-up month is billed at 75% of the monthly fee. We give you an exact quote after looking at your practice.
I'm leaving a hospital group to open a concierge practice. When should I reach out?
Ideally a few months before you open. We set up the business structure, books, payroll, and software so you start seeing patients with everything already in place. It's much easier than untangling it after the first year.
Our med spa has a management company and a separate medical entity. Can you handle both?
Yes. Many Illinois med spas are set up this way. We keep separate books for each entity and track the fees and transfers between them. Your attorney decides the structure, and we keep the records clean.
Can you calculate pay for our associate dentists or therapists?
Yes. We apply the terms of the compensation agreements you already have and run the resulting payroll. We don't design pay plans or advise on how providers should be paid, since those decisions fall under compliance rules your attorney should guide.
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