Hiring · 7 min read

Payroll Company vs CPA Payroll Services

You can run payroll through a dedicated provider like Gusto, ADP, or Paychex — or have your CPA's firm handle it directly. Both work. The right pick depends on the complexity of your situation, your need for tax planning integration, and how much you value a single point of contact.

What a payroll company gives you

  • Automated paycheck calculations and direct deposit
  • Federal, state, and local tax deposits filed automatically
  • Year-end W-2 and 1099 issuance
  • Employee self-service portals
  • Benefits, 401(k), and workers' comp integrations
  • Typical cost: $40–$150/mo base + $5–$15/employee

What CPA payroll services add

  • S-Corp reasonable compensation studies built in
  • Owner draw vs salary planning across the year
  • Multi-state payroll setup with nexus analysis
  • Fringe benefit and accountable plan structuring
  • Tax planning sessions that include payroll data
  • Single point of contact for tax + payroll + books

Where CPAs are stronger

When you're an S-Corp owner, run multiple entities, or operate across states, CPA-run payroll closes the gap between what gets paid and what gets taxed. The CPA can adjust reasonable comp mid-year if profit forecasts change, model owner-employee benefits, and ensure quarterly estimates account for actual payroll.

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  • Cash flow & owner pay basics

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Where payroll companies are stronger

For a stable W-2 team with no owner-comp complexity, dedicated payroll providers are cheaper, faster, and have better employee-facing tools. Gusto in particular has set the bar for self-service onboarding, benefits, and HR support.

What it actually costs

  • Gusto: $40/mo + $6/employee (Simple plan)
  • ADP RUN: ~$79/mo + $4–$12/employee, custom-priced
  • Paychex Flex: ~$39/mo + $5/employee, scales up
  • CPA-run payroll: $100–$400/mo for owner-only or small teams; more for larger payrolls

Frequently asked

Is CPA-run payroll worth the extra cost?

For S-Corp owners and multi-entity owners, yes. For a single LLC with W-2 staff and no owner draw complexity, a standalone payroll service is usually a better fit.

Can my CPA use Gusto on my behalf?

Many do — they run your payroll inside Gusto with their CPA partner account, giving you the software's automation and their tax oversight.

What about Patriot, OnPay, or Square Payroll?

All fine for small W-2 teams. Compare per-employee pricing and tax-filing inclusions before signing up.

Do I need separate workers' comp insurance?

Yes. Payroll services don't replace workers' comp; some integrate pay-as-you-go policies that pull premiums per payroll run.

What if I have remote employees in multiple states?

This is where CPA involvement pays off — registering for state withholding and unemployment in each state involves nexus decisions a payroll provider won't make for you.

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