Cheapest payroll for medical practice in 2026
Small medical, dental, and veterinary practices have payroll considerations general SMBs do not: HIPAA-sensitive employee data, multi-EIN setups across multiple practice locations, and provider-bonus structures tied to productivity. The cheapest legitimate option that handles all of this is OnPay; ADP Run is the safer choice for practices over 25 employees where compliance support matters.
Cheap payroll for medical practice, ranked
| Provider | 5 EE / mo | 10 EE / mo | Multi-EIN |
|---|---|---|---|
| Patriot Full Service | $57 | $77 | No (separate subscription per EIN) |
| Square Payroll | $65 | $95 | Yes |
| OnPay | $70 | $100 | Yes, native, no extra fee |
| Gusto Simple | $70 | $100 | No (Plus tier required) |
| Gusto Plus | $140 | $200 | Yes |
| QuickBooks Payroll Core | $75 | $105 | QBO bundle handles multi-entity |
| Paychex Flex Essentials | $64 | $89 | Yes with config |
| ADP Run Essential | $99 | $119 | Yes, native |
What you actually need from a payroll provider for HIPAA compliance
Employee payroll data (name, SSN, pay rate, deductions) is not Protected Health Information under HIPAA. PHI is patient health data: diagnoses, treatments, medical history. Standard payroll software does not touch PHI and does not need a BAA for the payroll function itself.
The HIPAA touchpoint comes in benefits administration. If your payroll provider is also handling health insurance benefits enrollment (collecting employee elections, transmitting them to the health plan), the enrollment data may include limited PHI. For benefits-bundled payroll, request a Business Associate Agreement (BAA) from the provider.
OnPay, Gusto, and ADP Run all sign BAAs on request for the benefits administration portion of their service. Patriot's BAA availability is less consistent. For a medical practice doing benefits enrollment through the payroll provider, OnPay or Gusto is the safer cheap choice.
The PLLC-per-location problem and how cheap payroll handles it
Medical and dental practices commonly operate as multiple PLLCs (Professional Limited Liability Companies), one per practice location or one per provider, for liability isolation and tax-planning reasons. Each PLLC has its own EIN and files its own payroll taxes.
Running payroll across multiple EINs on a single payroll provider account requires multi-EIN support. OnPay supports this natively at no extra cost: one OnPay account, multiple EINs, each EIN's employees on the correct tax filings. Gusto Plus ($80 + $12 per employee) supports multi-EIN; Gusto Simple does not. ADP Run handles multi-EIN cleanly across its full pricing range.
Patriot does not support multi-EIN on a single account. The workaround is a separate Patriot subscription per EIN. For a practice with 3 PLLCs, that is 3x the monthly fee, which closes the Patriot price advantage versus OnPay and may exceed it.
For a multi-EIN practice, OnPay is the cheapest payroll provider that handles the structure correctly. For a single-EIN practice, Patriot Full Service remains the cheapest sticker.
How to handle base + productivity bonus in cheap payroll
Medical and dental provider compensation often combines a base salary with a productivity bonus tied to RVUs, patient volume, or collections percentage. The bonus calculation typically happens monthly or quarterly outside the payroll provider, in the practice management system or a CFO spreadsheet.
Once you have the bonus dollar amount, the payroll provider treats it as a bonus pay item on the next payroll run. The provider calculates federal and state income tax withholding correctly (the IRS supplemental wage rate is 22 percent flat for amounts up to $1 million per year), plus FICA, plus any state withholding. Most cheap payroll providers handle this with a simple "bonus" pay-type option.
The complexity comes when the bonus structure includes deferred compensation, profit sharing, or 401(k) matching tied to bonus dollars. These add specific tax-treatment requirements. OnPay, Gusto, and ADP handle 401(k) integration with their partner providers. For complex deferred-comp structures, work with a tax adviser to confirm the payroll setup matches the plan document.
The practice size where ADP Run starts to make sense over OnPay
Most small medical practices (under 15 employees) are well-served by OnPay or Gusto Simple at $70 to $100 per month. The cheap-tier compliance is adequate, the multi-state handling is reliable, and the support is responsive.
Once a practice grows past 20 to 25 employees, the case for ADP Run starts to land. ADP's dedicated specialist support means a named contact at ADP who knows your practice setup, multi-EIN structure, and provider bonus schedule. For practices where payroll mistakes are expensive (a misclassified provider tax can be $10,000+ to unwind), the specialist support is worth the $20 to $40 per month premium over OnPay.
ADP Run at 25 employees is typically quoted around $179 per month. OnPay at 25 employees is $190 per month. At that size, the price is essentially tied and the choice comes down to support model preference. Below 25 employees, OnPay is meaningfully cheaper. Above 50 employees, ADP Workforce Now (the mid-market product) starts to be the right answer regardless of price.
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Common questions
What is the cheapest payroll service for a small medical practice?
OnPay at $40 + $6 per employee handles single-EIN practices cleanly at the cheapest done-for-you-tax price. For a 10-employee practice that is $100 per month. Gusto Simple matches at $100 if single-state. Patriot Full Service at $77 is the absolute cheapest but lacks the multi-EIN and provider-bonus depth medical practices often need.
Does payroll software need to be HIPAA compliant?
Payroll software stores employee data (name, SSN, address, pay rate). Employee data is not technically Protected Health Information under HIPAA. However, dental and medical practices often use payroll providers to handle benefits enrollment, which can touch health plan election data that does have HIPAA implications. Most cheap payroll providers (OnPay, Gusto, ADP) sign BAAs (Business Associate Agreements) when requested. Patriot's BAA availability is less consistent.
Can I run payroll across multiple PLLCs on one bill?
Yes if the provider supports multi-EIN. OnPay supports it natively. Gusto requires Plus tier for multi-EIN. ADP Run handles multi-EIN cleanly. Patriot does not support multi-EIN on a single account; you would run a separate Patriot subscription per PLLC.
How do provider productivity bonuses work in payroll?
Provider compensation often combines base salary with productivity bonuses tied to RVUs (Relative Value Units), patient volume, or collections percentage. The bonus calculation happens outside payroll (in your practice management system or a spreadsheet) and the resulting bonus amount is entered as a payroll item. Most cheap payroll providers handle this as a standard bonus pay item; the calculation is your problem.
Should I use a medical-specific payroll provider?
Generally not necessary. Medical-specific HR and payroll tools like Practice EHR's payroll module or Greenway Health are bundled with practice management software and priced accordingly. For payroll alone, OnPay and Gusto are meaningfully cheaper and handle the medical-specific needs at the standard tier.
What about associate dentist or veterinarian compensation?
Associate compensation is often a hybrid: base salary plus percentage of collections. The payroll calculation is the same as provider productivity bonuses: calculate the variable portion outside payroll, enter as a bonus item, payroll calculates the tax withholding correctly. OnPay and Gusto both handle bonus pay items cleanly.