Independent Certified QuickBooks ProAdvisor firm · U.S.-based

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 payments that arrive partial, adjusted, and weeks late. A named Certified QuickBooks ProAdvisor reconciles payer deposits to billing, tracks the books inside your PC or PLLC structure, and keeps the financials your CPA needs clean — month after month.

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The short version.

Medical practice accounting in New York is defined by the revenue cycle, not the expense side. Insurance and payer deposits arrive partial, adjusted by contractual write-offs, and weeks after service — so reconciling what was billed to what was actually collected is the central job, and it's where most practices lose visibility. New York adds a structural layer: under the state's Corporate Practice of Medicine doctrine, a medical practice must be owned by licensed physicians through a Professional Corporation (PC) or PLLC, not a standard LLC, and revenue can't be shared with non-physicians — which shapes how the books and any management-company arrangement are structured. A named Certified QuickBooks ProAdvisor reconciles payer deposits to billing, tracks the books inside your professional entity, handles practice payroll, and keeps monthly financials clean for your CPA. We don't set up the entity or give legal advice — your attorney and CPA do that; we do the books inside it. Fixed-fee at $400–$2,500+/mo, all 62 counties. We do the books; your CPA files.

Quick answers

New York medical practice accounting, in five questions.

What's different about accounting for a medical practice?

The revenue cycle. Insurance and payer deposits arrive partial, reduced by contractual adjustments, and weeks late — so the core work is reconciling what was billed to what was actually collected, by payer. Generalist bookkeeping that just records the deposit misses the write-offs and the gaps.

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

Yes. Under New York's Corporate Practice of Medicine rules, a practice must be physician-owned through a Professional Corporation (PC) or PLLC — not a standard LLC — and medical revenue can't be shared with non-physicians. Your attorney sets the structure; we keep the books inside it.

Cash basis or accrual?

Many small practices run cash basis for simplicity, but accrual shows the truer picture when large receivables sit unpaid with payers. We keep the books so your CPA can report on the basis that fits — and see both.

What does it cost?

$400–$2,500+/mo, fixed-fee against a written scope, set by visit volume, number of providers, and payer complexity.

Can you reconcile insurance payments to my billing system?

Yes — that's the core of it. A named Certified ProAdvisor reconciles payer and patient deposits against your practice-management or billing system, separating contractual adjustments from true revenue, so your books reflect what you actually earned and collected.

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 of these you're in tells us where to start.

  • Revenue is a black box

    Payer deposits aren't reconciled to billing.

    Most common · nearly every practice

    The problem: 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: Payer and patient deposits reconciled against your billing or practice-management system, with contractual adjustments separated from real revenue.

    Honest read: 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.

    High impact · insurance-heavy practices

    The problem: 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: Books kept so your CPA can report on cash or accrual as fits, with aged receivables by payer so the revenue pipeline is visible.

    Honest read: 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.

    Rising risk · group & MSO arrangements

    The problem: 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: 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.

    Honest read: 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

New York medical practice accounting, done by an expert.

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

Tools we work alongside

Connected to how you run the practice.

  • QuickBooks Online
  • athenahealth
  • DrChrono
  • Kareo / Tebra
  • SimplePractice
  • Square
  • Stripe
  • Gusto

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 discovery 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.

  1. 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.

  2. 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.

  3. Phase 3

    Monthly close & reporting

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

  4. Phase 4

    Reporting & advisory

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

Book a Discovery Call

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 Certified ProAdvisor who knows your practice's numbers turning them into collection-rate analysis, provider profitability, and cash-flow forecasting. Automation handles the data entry. We handle the judgment. As automation takes over routine entry, this judgment layer is where practices find their edge.

Explore fractional CFO & advisory →

Common questions

New York medical practice accounting questions.

The revenue cycle. Unlike most businesses, a practice rarely collects what it bills at the time of service — insurance pays a contracted amount, net of adjustments and denials, often weeks later, with the patient responsible for the balance. So the central accounting work is reconciling what was billed to what was actually collected, by payer, and separating contractual write-offs from true revenue. Generalist bookkeeping that simply records the deposit misses all of that, which is why practices need accounting built around the payer side.

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.

Many smaller practices use cash basis because it's simpler and aligns with when money actually arrives. But because practices carry large receivables waiting on payers, accrual often shows a truer picture of what the practice has earned and is owed. The right answer depends on your size and how your CPA files, and the two aren't mutually exclusive in management reporting. We keep the books so your CPA can report on the basis that fits and so you can see receivables either way — your CPA confirms the basis for your tax filing.

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.

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.

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.

Monthly bookkeeping for a New York medical practice runs $400–$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.

Book 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 named Certified ProAdvisor begins as soon as you approve. We do the books; your CPA files and confirms your accounting basis and entity matters.

Page review & standards

Reviewed by the TechBrot Certified ProAdvisor team.

Reviewed and maintained by the accounting team at TechBrot Inc., an independent Certified QuickBooks ProAdvisor firm serving New York medical and healthcare practices remotely. Pricing reflects TechBrot's New York engagement ranges; New York Corporate Practice of Medicine and entity references reflect rules current as of the date below and are reviewed periodically. TechBrot provides bookkeeping inside your established professional entity; entity setup and legal structure are handled by your attorney, and your CPA confirms accounting basis and files.

Reviewer

David Westgate · 40+ years operational accounting experience

Standards

Fixed-fee, written scope · Client retains QuickBooks ownership · Entity & legal structure handled by your attorney · No legal or tax-filing advice (out of scope) · No fabricated data

Last reviewed: June 2026

Related

Related New York services & industries.

See what your practice actually collects.

Book a free books review. We'll look at your QuickBooks file and payer reconciliation, show you where revenue and collection gaps are hiding, and send a written fixed-fee quote within 3 business days. No pitch.

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TechBrot is an independent Certified QuickBooks ProAdvisor firm. We provide bookkeeping, QuickBooks, payroll, and advisory services and coordinate with your CPA or EA. We do not provide legal advice, set up professional entities, file tax returns, or represent clients before tax authorities. QuickBooks is a registered trademark of Intuit Inc.; TechBrot is not affiliated with Intuit Inc.