How much does it cost to have a CPA run my payroll?

Most CPAs charge a base fee of $50-$150 per payroll run plus $5-$15 per employee. For a small business with 5 employees running biweekly payroll, that works out to roughly $200-$400 per month, or $2,400-$4,800 per year. CPAs that bundle payroll into a monthly accounting retainer often quote $300-$600/month all-in.

Is it cheaper to use Gusto or ADP than a CPA for payroll?

Pure software is cheaper on paper. Gusto runs $40-$80/month base plus $6-$12 per employee, and ADP Run starts around $79/month plus $4-$5 per employee. A CPA typically costs 2-3x more but includes tax filings, year-end reconciliation, owner W-2/K-1 coordination, and tax planning. For businesses under 10 employees, a CPA usually pays back the difference in caught errors and integrated tax work.

What is included in CPA payroll services?

A standard CPA payroll engagement includes calculating gross-to-net pay, withholding federal and state income tax, Social Security and Medicare, filing Form 941 quarterly, Form 940 annually, state unemployment returns, issuing W-2s and 1099s, direct deposit setup, and handling new-hire reporting. Most CPAs also reconcile payroll to the general ledger monthly.

Do CPA payroll fees include the cost of paying employees?

No. The CPA fee covers preparation, filing, and compliance. The actual wages, employer payroll taxes (7.65% FICA match plus federal and state unemployment), and any benefits costs are paid out of your bank account separately. Budget those at roughly 10-12% on top of gross wages.

When should a small business switch from DIY payroll to a CPA?

Most CPAs recommend outsourcing once you have 3 or more employees, operate in multiple states, run an S-corp where the owner takes a reasonable salary, or have ever missed a 941 deposit deadline. The IRS trust-fund recovery penalty is 100% of unpaid payroll taxes, which makes DIY mistakes more expensive than 12 months of CPA fees.

How Much Do CPA Payroll Services Cost for a Small Business in 2026?

May 30, 2026 · Cost Guide · 5 min read

Payroll is the most common service small businesses outsource to their CPA, and also the one where pricing is the most opaque. Software providers advertise a flat monthly rate; CPAs usually quote a base plus per-employee fee plus year-end work. This guide breaks down what you should actually pay in 2026, what should be included, and when paying a CPA beats running it yourself through Gusto, ADP, or QuickBooks Payroll.

Average CPA Payroll Pricing in 2026

Across small-firm CPAs in the United States, payroll pricing typically falls into three structures:

Per-payroll-run pricing: $50-$150 base per run plus $5-$15 per employee. A 5-person company on biweekly payroll pays roughly $200-$400/month.
Flat monthly retainer: $250-$700/month for full payroll service including tax filings. Most common at firms that also handle your bookkeeping.
Bundled into a CFO/advisory retainer: $1,500-$4,000/month for businesses with $1M-$5M in revenue, where payroll is a line item inside a broader engagement.

Year-end work — W-2s, 1099s, Form 940, state reconciliations — is usually billed separately at $150-$500, depending on how many employees and contractors you have.

What's Included at Each Price Point

Basic Payroll ($150-$300/month)

This is the entry-level tier most local CPAs offer. You get:

Gross-to-net pay calculations
Federal and state withholding
Direct deposit setup and processing
Quarterly Form 941 filing
Annual Form 940 (FUTA) filing
State unemployment filings
W-2 and 1099-NEC issuance in January

What's typically not included: multi-state filings, benefits administration, garnishments, retirement plan contributions, or HR support.

Full-Service Payroll ($350-$700/month)

Adds:

Multi-state withholding and filings
401(k) and SEP-IRA contribution remittance
Garnishment and child-support processing
Workers' comp audit support
New-hire reporting in every state
Owner reasonable-salary review (for S-corps)
Year-end W-2/W-3 reconciliation to the books

Bundled Accounting + Payroll ($600-$1,500/month)

For most growing businesses, this is where the math gets attractive. A CPA managing both your bookkeeping and your payroll catches errors that a standalone payroll provider never sees — like an owner draw being mis-classified as wages, or contractor payments crossing the $600 1099 threshold without anyone noticing.

CPA vs. Payroll Software: A Real Cost Comparison

Here's what a 6-employee S-corp with one owner on payroll actually pays in 2026:

Provider	Base/Month	Per Employee	Total/Month	What You Get
Gusto Simple	$40	$6	$76	Software only, no advisory
Gusto Plus	$80	$12	$152	Multi-state, time tracking
ADP Run Essential	$79	$4	$103	Software + basic support
QuickBooks Payroll Premium	$85	$9	$139	Software, QBO integration
Local CPA (basic)	$150	$10	$210	Filings + reconciliation
Local CPA (full-service)	$350	$15	$440	Multi-state, S-corp planning, audit support

The software providers look cheaper because they don't include the tax planning, reasonable-salary reviews, and year-end clean-up that a CPA does as part of the engagement. Most small businesses end up paying a CPA $500-$1,200 at year-end to clean up a software-only payroll anyway, which closes most of the gap.

When a CPA Beats Software

You should be running payroll through a CPA — not just software — if any of the following apply:

You're an S-corp owner. Setting the wrong reasonable salary is one of the top S-corp audit triggers. A CPA benchmarks your salary annually using Bureau of Labor Statistics data and documents the rationale, which is exactly what the IRS asks for if challenged.
You operate in multiple states. Each state has its own withholding, unemployment, and reciprocity rules. Software handles the mechanics but rarely flags nexus issues that create new state filing obligations.
You issue both W-2s and 1099s. Misclassifying a contractor as an employee (or vice versa) triggers IRS Form SS-8 reviews and state Department of Labor inquiries. CPAs flag the risk; software just processes the form you select.
You've ever missed a deposit. Federal payroll tax deposits are due semi-weekly or monthly depending on your lookback period. Missing one triggers a 2-10% failure-to-deposit penalty plus the trust-fund recovery penalty — a personal liability against owners and officers equal to 100% of the unpaid tax.

When Software-Only Is Enough

You probably don't need a CPA running payroll if:

You're a single-member LLC with no employees (you don't run payroll on yourself)
You have 1-2 W-2 employees in a single state
You're not an S-corp or C-corp owner taking a salary
Your CPA already reviews your books quarterly and would catch payroll errors in that review

In those cases, Gusto, ADP Run, or QuickBooks Payroll will handle the mechanics for $80-$150/month, and you can have a CPA review at year-end for an extra $300-$500.

Hidden Costs That Surprise Small Businesses

Off-cycle payrolls: Bonuses, final paychecks, or correction runs are billed at $50-$150 each on top of the base.
Multi-state setup: Adding a new state typically costs $150-$400 in registration, account setup, and the first filing.
Year-end W-2/1099 packages: $5-$15 per form, with a $150 minimum at most firms.
Workers' comp audit support: $250-$750 if your insurer audits your wages, which most do annually.
Catch-up filings: If you switch CPAs mid-year, expect $500-$1,500 to reconcile and refile any prior-quarter errors.

How to Get an Accurate Quote

Before you sign a payroll engagement letter, ask any CPA for an itemized quote that answers:

What's the per-payroll-run base fee and what's the per-employee charge?
What's included at year-end, and what's billed extra?
Are quarterly state and federal filings bundled or separate?
What does an off-cycle payroll cost?
Do you reconcile payroll to the general ledger monthly?
Will you represent us in a workers' comp audit, IRS payroll review, or state unemployment audit?

If you're comparing CPA-managed payroll against software, the real question isn't price per month. It's total cost of ownership including year-end clean-up, audit risk, and the time you'd otherwise spend on filings.

Finding a CPA That Handles Payroll Well

Not every CPA offers payroll — many smaller firms outsource it to Gusto or ADP under their own brand. If integrated payroll matters to you, ask explicitly whether they process payroll in-house or refer it out, and what the markup is either way.

Ready to compare CPAs? Browse our directory by location to find firms in your market: CPAs near you, Atlanta, or all cities. For broader pricing context, see our CPA cost guide and how much a small-business CPA costs.

Frequently Asked Questions

How much does it cost to have a CPA run my payroll?: Most CPAs charge a base fee of $50-$150 per payroll run plus $5-$15 per employee. For a small business with 5 employees running biweekly payroll, that works out to roughly $200-$400 per month, or $2,400-$4,800 per year. CPAs that bundle payroll into a monthly accounting retainer often quote $300-$600/month all-in.
Is it cheaper to use Gusto or ADP than a CPA for payroll?: Pure software is cheaper on paper. Gusto runs $40-$80/month base plus $6-$12 per employee, and ADP Run starts around $79/month plus $4-$5 per employee. A CPA typically costs 2-3x more but includes tax filings, year-end reconciliation, owner W-2/K-1 coordination, and tax planning. For businesses under 10 employees, a CPA usually pays back the difference in caught errors and integrated tax work.
What is included in CPA payroll services?: A standard CPA payroll engagement includes calculating gross-to-net pay, withholding federal and state income tax, Social Security and Medicare, filing Form 941 quarterly, Form 940 annually, state unemployment returns, issuing W-2s and 1099s, direct deposit setup, and handling new-hire reporting. Most CPAs also reconcile payroll to the general ledger monthly.
Do CPA payroll fees include the cost of paying employees?: No. The CPA fee covers preparation, filing, and compliance. The actual wages, employer payroll taxes (7.65% FICA match plus federal and state unemployment), and any benefits costs are paid out of your bank account separately. Budget those at roughly 10-12% on top of gross wages.
When should a small business switch from DIY payroll to a CPA?: Most CPAs recommend outsourcing once you have 3 or more employees, operate in multiple states, run an S-corp where the owner takes a reasonable salary, or have ever missed a 941 deposit deadline. The IRS trust-fund recovery penalty is 100% of unpaid payroll taxes, which makes DIY mistakes more expensive than 12 months of CPA fees.