Payroll for accountants and bookkeepers: partner programs, client costs and what to ask

Quick picks

Published accountant program terms

OnPay onlyvolume discount or revenue share

Lowest retail per 5-person client

$62/moPatriot Full Service

State registration done for you

GustoMiddesk or $85/state/mo

Prices checked

Oct 16, 2026vendor pricing pages

• Patriot Software: low-cost option for very small clients.
• Gusto: client self-service and state registration.
• OnPay: a flat price across states.
• QuickBooks Payroll: clients already on QuickBooks Online.
• ADP RUN: when the client wants a phone rep.

This page has two audiences. If you run an accounting or bookkeeping firm, the sections on partner programs, multi-client costs and notice windows are for you. If you are a business owner looking for payroll and bookkeeping services, skip to the owner section further down for what to ask a firm that runs payroll for you.

Scores

Scores follow our scoring method. Our full payroll ranking is on best payroll software.

The providers

What multi-client payroll costs at retail

Retail is the ceiling. An accountant program can lower it, but only OnPay states what it offers (a volume discount or a revenue share), and none of these providers publishes a rate. Ask each for the discount as a percentage, whether it lasts or expires, and whether the firm or the client is billed. For other headcounts, see the payroll cost guide.

Per-client fees firms forget to pass through

• Extra states: QuickBooks and Patriot $12 a month per state, SurePayroll $9.99. Gusto Simple is one state only.
• Year-end forms: Square charges $3 per mailed paper W-2 or 1099; SurePayroll bills $50 plus $5 per form each year.
• Offboarding: Gusto charges $100 federal, $100 per state and $5 per form to file final returns; QuickBooks charges $150 for year-end forms after cancellation.

Referral and partner payouts

Referral payouts can conflict with your duty to a client. If you take a referral fee, tell the client in writing. Paychex's PEO terms already bar taking a second commission tied to the same client.

What matters when you run payroll for clients

• Notice windows. If notices come to your firm, the guarantee clock is running. Gusto needs notice 30 days before the agency response date; QuickBooks Elite needs the notice emailed within 15 days of its date.
• The tax stays with the client. Outsourcing payroll does not move the client's employment tax liability unless the provider is an IRS-certified PEO (26 USC 3511). Every guarantee we read excludes errors from data the client or firm entered.
• State registration. Only Gusto registers state accounts for clients. Paychex, QuickBooks and ADP expect the ID numbers from you.
• Year-end deadlines. 2026 Forms W-2, W-3 and 1099-NEC are due February 1, 2027. The 1099-NEC threshold rises to $2,000 for 2026 payments, and e-filing is required at 10 or more information returns in total.
• Record access after a client leaves. QuickBooks keeps payroll data for one year after cancellation; Wave access ends at month end; Patriot keeps forms downloadable; Gusto admins keep limited read-only access.
• Switching a client mid-year. Load year-to-date totals so the $184,500 Social Security wage base is not overpaid, and agree who files the open quarter. Our payroll outsourcing guide has the full checklist.

For business owners: payroll and bookkeeping services

Many bookkeepers and CPA firms run payroll for clients, usually on one of the platforms above. We did not find published fee data for firm-run payroll in our research, so we do not quote a range. You can work out the floor yourself: the platform's retail fee (for a 5-person company, $62 to $140 a month in the table above) plus the firm's time.

What to ask a firm

• Which payroll platform do you use, and is the account in my company's name with my own login?
• Do you pass through the platform's price, mark it up, or receive a referral fee or discount?
• Who receives agency notices, and how fast do you forward them? (Gusto's guarantee needs notice 30 days before the deadline.)
• Who registers new state accounts when I hire out of state?
• If I leave your firm, can I keep the payroll account and download every W-2, 941 and register?

If you would rather run it yourself, compare in-house vs. outsourced payroll or start with payroll for small teams.

Common mistakes

• Putting client payroll accounts in the firm's name, which makes it hard for a client to leave cleanly.
• Missing a guarantee notice window because agency mail sat in the firm's inbox.
• Comparing base fees only. At 5 employees the per-person fee is $30 of Gusto Simple's $79.
• Not budgeting offboarding fees, such as Gusto's $100 federal and $100 per state for final returns.
• Taking a referral payment without telling the client.