New York · Healthcare & Medical Practices

New York medical practice accounting that handles payers, not just expenses.

For practices, clinics, and group providers, the hard part is the revenue — insurance that arrives partial, adjusted, and weeks late. Your senior bookkeeper reconciles payer deposits to billing, keeps the books inside your PC or PLLC structure, handles provider and staff payroll, and keeps the financials your CPA needs clean — all in your own QuickBooks file, with every close reviewed by a Certified QuickBooks ProAdvisor before it reaches you.

New York rule: a physician may not let non-licensees share professional fees, including by paying for space, equipment or staff as a percentage of, or dependent on, practice income; rent and management fees post as fixed amounts, never computed from collections. Source: NY Education Law §6530(19).

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Bookkeeping & advisory · Fixed-fee · written scope within 3 business days

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§The short version

New York medical-practice accounting from TechBrot reconciles what was billed to what each payer actually paid, separates contractual adjustments from true revenue and tracks aged A/R by payer, alongside provider compensation and payroll, with PC/PLLC books that keep management and rent fees at fixed amounts. Monthly bookkeeping runs $500–$2,500+/mo, in your own QuickBooks file.

§Why NY practice books mislead

Three places New York practices lose the real numbers.

A busy practice can look profitable while receivables age and write-offs go untracked. Knowing which one you’re in tells us where to start.

Revenue is a black box

Payer deposits aren’t reconciled to billing.

An insurance deposit is rarely the amount billed — it’s net of contractual adjustments, denials, and patient responsibility, often weeks after the visit. Record the deposit as revenue and you lose the write-offs, can’t see your true collection rate, and never know which payers underpay. The fix is payer and patient deposits reconciled against your billing or practice-management system, with contractual adjustments separated from real revenue. If your books show the deposit but not what was billed and adjusted, you can’t tell a slow payer from a lost one.

Cash flow looks wrong

Receivables and basis aren’t managed.

With large balances sitting unpaid in accounts receivable, cash-basis books can make a strong month look weak or a weak one look fine. Without an aged A/R view by payer, you can’t see how much revenue is stuck in the pipeline or where collections are stalling. The fix is books kept so your CPA can report on cash or accrual as fits, with aged receivables by payer so the revenue pipeline is visible. If you don’t know your A/R by payer right now, your cash-flow picture is part guesswork.

NY structure risk

Books don’t fit the PC/PLLC structure.

New York requires a medical practice to be physician-owned through a PC or PLLC, and prohibits sharing medical revenue with non-physicians. When a practice works with a management company (MSO) or grows into a group, books that don’t cleanly separate clinical revenue from administrative fees can blur a line the state takes seriously. The fix is books structured to fit your professional entity and to keep any management-fee arrangement cleanly separated — set up with your attorney and CPA, maintained accurately by us. The entity and any MSO structure is a legal decision for your attorney; our job is books that reflect it correctly, not muddy it.

§What TechBrot handles

How we keep a New York medical practice’s books.

Every engagement is scoped to your providers and payer mix, delivered in your own QuickBooks file by your TechBrot team, with every close reviewed by a Certified QuickBooks ProAdvisor — coordinating with your CPA, who files.

01 · Payer reconciliation

Insurance & patient deposits

Payer and patient deposits reconciled to your billing system, with contractual adjustments separated from true revenue so collection reality is visible.

New York reconciliation →

02 · Accounts receivable

Aged A/R by payer

Receivables tracked and aged by payer so you can see how much revenue is in the pipeline and where collections are stalling.

New York monthly bookkeeping →

03 · Entity-fit books

PC / PLLC bookkeeping

Books structured to fit your physician-owned professional entity, with clinical revenue and any management-fee arrangement cleanly separated.

New York QuickBooks setup →

04 · Practice payroll

Provider & staff payroll

Payroll for physicians, NPs, PAs, and administrative staff handled correctly, with the W-2-vs-1099 worker-classification care New York enforces closely — including per-diem and locum providers.

Payroll management →

05 · Provider profitability

Profit by provider or location

QuickBooks classes and tags configured so a group or multi-location practice can see profitability by provider, location, or service line — not just a blended total.

New York bookkeeping →

06 · Cleanup & catch-up

Back-books & reconstruction

Behind on the books or carrying months of unreconciled payer deposits? We rebuild them CPA-ready, separating adjustments from revenue, then keep them clean.

New York bookkeeping cleanup →

§Revenue and fee books

Payer, provider and fee books built for New York.

Your books are prepared by a senior bookkeeper matched to your industry and software, or by a specialist partner practice when your books need one, working only from the financial summaries your billing system exports, never from patient records. Four pieces carry most of the weight:

Claims → remittances → deposits

Every remittance tied to a deposit

Each payer’s remittance totals are matched to the claims they pay and to the EFT or lockbox deposit that carried them. Contractual adjustments, denials, recoupments and patient balances post to their own accounts, so a short payment or a takeback shows up the month it happens.

Provider compensation

Compensation from figures that tie

Charges, adjustments and collections are reported by rendering provider each month from the billing summaries, reconciled to what payers actually deposited, so a collections-based or production-based compensation formula runs on numbers the bank agrees with.

Education Law §6530(19)

Management and rent fees at fixed amounts

Management-company fees, rent and equipment or staffing charges are booked as the fixed amounts the contracts set, each in its own account, with the contracts on file. A charge that moves with collections is flagged to you and your attorney, because New York treats a percentage-of-income payment for space, equipment or personnel as fee-splitting.

Credit balances

Overpayments held as liabilities

Patient credit balances and payer overpayments sit in liability accounts until they are refunded or applied, aged monthly, so they never inflate revenue and the refund trail is ready if a payer asks.

§Tools we work alongside

Connected to how you run the practice.

QuickBooks Online — the practice ledger payer deposits reconcile into
athenahealth — deposits and adjustments exported to QuickBooks
DrChrono — EHR and billing reconciled to the books
Kareo / Tebra — practice-management payments matched to deposits
SimplePractice — behavioral-health billing reconciled
Square — patient copays and card payments
Stripe — online patient payments
Gusto — provider and staff payroll

Using a different EHR or practice-management system? If it exports deposits and adjustments to QuickBooks, we can build the workflow around it. Ask on a call.

§How engagements work

From mystery deposits to a clear revenue picture.

Every New York medical-practice engagement follows the same four-phase rhythm — books accurate first, revenue visibility second, advisory third.

Phase 1

Discovery

A 30-minute call to map your payer mix, billing system, entity structure, provider count, and where the books stop reflecting reality. No pitch.

Phase 2

Setup & cleanup

Configure payer-reconciliation workflows and entity-fit books, plus a cleanup to reconcile prior payer deposits and separate adjustments from revenue.

Phase 3

Monthly close & reporting

Monthly reconciliation of payer and patient deposits, aged A/R by payer, provider and staff payroll, and provider- or location-level reporting where you want it.

Phase 4

Reporting & advisory

Collection-rate and provider-profitability reporting and, as the practice grows, cash-flow and expansion advisory.

§Beyond the books

A clear revenue picture is the start. Running a healthy practice is the point.

Once payer deposits reconcile, receivables are visible by payer, and your books fit your entity, the question shifts from “what did we actually collect?” to “how do we run this better?” Which payers are worth the administrative burden, where the collection rate is leaking, whether a provider or location is carrying the practice or dragging it, when cash flow supports adding staff or space — the decisions that separate New York practices that thrive from those that just stay full.

That’s where advisory comes in: a QuickBooks ProAdvisor who knows your practice’s numbers turning them into collection-rate analysis, provider profitability, and cash-flow forecasting. As automation handles routine data entry, this judgment layer is where practices find their edge. Explore fractional CFO & advisory →

Get the free file review

Checked against New York Education Law §6530(19) and the Department of State’s PC / PLLC guidance.

Published: 2026-06-07Updated: 2026-10-21

§Questions

New York medical practice accounting questions.

Does New York require a special business entity for a medical practice?

Yes. Under New York’s Corporate Practice of Medicine rules, a medical practice must be owned and controlled by licensed physicians and structured as a Professional Corporation (PC), a Professional Limited Liability Company (PLLC), or a professional partnership — not a standard LLC or general business corporation. New York also prohibits sharing medical-service revenue with non-physicians, which is why arrangements with management companies (MSOs) must keep clinical services and administrative fees clearly separate. Setting up the entity and any MSO structure is a legal matter for your attorney and CPA; our role is keeping the books accurate inside whatever structure they establish.

Can you reconcile insurance payments to my billing or EHR system?

Yes — it’s the heart of medical-practice bookkeeping. We reconcile payer and patient deposits against your practice-management or billing system, separating the contractual adjustment (the difference between billed and contracted rates) from true revenue and from denials. Done right, your books show what you actually earned and collected, your collection rate by payer becomes visible, and you can spot payers who consistently underpay or delay. We work alongside systems like athenahealth, DrChrono, Kareo/Tebra, and others that export deposits and adjustments.

Do you handle payroll for physicians and clinical staff?

Yes. We handle payroll for physicians, nurse practitioners, physician assistants, and administrative staff, integrated into the same QuickBooks file as your bookkeeping. New York enforces worker classification closely, so we keep employee versus contractor treatment clean — which matters for practices that use per-diem providers or independent contractors alongside W-2 staff. Payroll is scoped alongside the core bookkeeping engagement.

Can you show profitability by provider or location?

Yes. For group practices and multi-location providers, we configure QuickBooks classes and tags so you can pull profitability by provider, location, or service line rather than only a blended practice total. That’s what lets you see which providers or sites are carrying the practice, where overhead is concentrated, and how compensation should track contribution — the visibility that supports both day-to-day decisions and partner or associate compensation discussions.

Can a management company be paid a percentage of our collections in New York?

That is a legal question for your attorney, and the statute is the place to start. New York Education Law §6530(19) makes it professional misconduct for a physician to let anyone outside a short list of licensed colleagues share in the fees for professional services, and it expressly includes any arrangement in which the payment for space, facilities, equipment or personnel services is a percentage of, or otherwise dependent on, the licensee’s income or receipts from the practice, with an exception for facilities licensed under article 28 of the Public Health Law and article 13 of the Mental Hygiene Law. In the books, we record management, rent and equipment or staffing fees as the fixed amounts your contracts set, each in its own expense account, and we flag any charge that rises and falls with collections to you and your attorney instead of simply paying it.

How do you report provider compensation inside a New York PC or PLLC?

From the professional entity’s own books. Each month we report charges, contractual adjustments and collections by rendering provider from the billing system’s financial summaries, reconciled to the payer deposits that landed in the PC or PLLC’s account, so a collections-based or production-based formula pays physicians, NPs and PAs from figures the bank agrees with. Payments that leave the entity for an MSO, landlord or staffing company stay on their own fixed-fee lines, apart from provider pay. The formula itself comes from your provider agreements and your attorney; we supply the numbers it runs on and keep provider pay clean in payroll.

How much does medical practice bookkeeping cost in New York?

Monthly bookkeeping for a New York medical practice runs $500–$2,500+ per month, fixed-fee against a written scope. Pricing is set by visit and transaction volume, the number of providers, payer complexity, and whether you need provider- or location-level reporting — a solo practitioner is at the lower end; a multi-provider group with complex payer mix higher. We quote a firm number after reviewing your books.

How do we get started?

Start with a free discovery call. We review your QuickBooks file and billing system remotely, map your payer mix and entity structure, determine whether you need a cleanup first or can go straight to monthly service, and send a written fixed-fee proposal within 3 business days. Your senior bookkeeper begins as soon as you approve.

§Around this page

Around New York.

New York QuickBooks ProAdvisor & bookkeeping

The state page: services, industries, cities and the New York tax terms in one place.

Healthcare accounting, nationally

The national engagement this page is the New York version of — same scope, same written fixed fee.

Also in New York: Bookkeeping services · Monthly bookkeeping.

Other New York industries: Construction · Consulting · Ecommerce · Legal · Nonprofit · Real estate · Restaurant · all New York industries.

New York cities: Buffalo · Brooklyn · Queens · every New York city page — served remotely, in your own QuickBooks file.

Not sure where your file stands? Start with the free QuickBooks file review · how New York compares: state-by-state tax quirks.

New York practices start here

See what your practice actually collects.

What happens after you call.
1. We talk for up to 30 minutes. You tell us where the books stand; we ask the questions that decide the scope. No charge.
2. We look at the file if we need to. You add us as an accountant user in your own QuickBooks file, and you can remove us at any time. If the file cannot be priced without working inside it, we say so and propose the paid diagnostic, whose fee is credited in full against the cleanup.
3. You get a fixed fee in writing. What we will fix, what you will receive and one fixed fee. Nothing starts until you accept it.