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If you are a CPA, a bookkeeper or an accounting firm, you choose payroll software twice. Once for the firm: can you manage every client from one login, give your staff the right access, and decide who gets the bill? And once for each client: does it file in the states where they have staff, issue W-2s and 1099s, and post to the accounting software you already keep their books in? This guide answers both for the US payroll tools SMB Compare lists.
It is written for the people running payroll on clients' behalf. If you are a business owner choosing payroll for your own company, our guide to payroll software for small business is the one to read.
How we chose. The cost table runs all 12 payroll providers we list for US businesses through the engine behind the payroll software comparison. A firm judges payroll twice, across its whole client book and client by client, so the picks rest on a multi-client view for the firm, then federal and state filing, year-end W-2s and 1099s, and a sync to the ledger the firm already keeps for each client. The table above opens on one client with 5 employees; set it to a client's headcount and it re-prices. It shows each provider's list price to the client, before any partner discount or revenue share. Affiliate status never changes the picks or their order.
Client payroll for CPAs and bookkeepers: multi-state filing and the multi-client view
A US accounting firm needs client payroll software that does two jobs: run each client's pay runs and federal, state and multi-state filings correctly, and let the firm manage many clients without a separate login for each. The first is in every full-service product; the second differs by vendor, and our comparison data does not hold it, so the firm-level detail below comes from the vendors' own accountant pages.
Start with the client-level features, with our wording intact:
| Provider | Full-service tax filing | Multi-state payroll | Benefits administration |
|---|
| OnPay | Yes | Yes | Yes |
| QuickBooks Payroll | Yes | Yes | Yes |
| Patriot Software | Yes (Full Service) | Yes | Limited |
| Homebase | Yes | Yes | Limited |
| Gusto | Yes | Yes (Plus) | Yes |
A plan name in brackets means the feature starts on that plan. "Limited" means some help short of full administration: at Homebase it is individual-market health coverage rather than a group plan, and at Patriot Software it is an HR add-on. "Yes (Full Service)" at Patriot means filing is on its Full Service tier and not on Basic.
Then the firm-level features. OnPay says on its accountant page that one dashboard shows every client, with multiple permission levels so a firm can keep control, delegate to its own staff or hand payroll duties to the client. QuickBooks Payroll is added to a client from QuickBooks Online Accountant or Intuit Accountant Suite, the firm logins Intuit names on its payroll page for accountants. Ask any other vendor to demonstrate its multi-client view before you move a client book onto it.
Accountant partner programs: discounts, revenue share and who bills the client
Two providers' terms for accounting firms are ones we could read on the vendor's own page: OnPay's and QuickBooks'. Both let a firm choose between passing a discount to the client and keeping a share of the subscription, and both let either the firm or the client pay. Neither discount appears in the cost table above, which shows list prices.
OnPay's program has four levels, set by how many clients you run on it, as its accountant page showed when we read it in October 2026:
| Clients on OnPay | Level | Discount |
|---|
| 1 to 2 | Member | None listed |
| 3 to 19 | Preferred | 10% |
| 20 to 49 | Advanced | 15% |
| 50+ | Elite | 20% |
Every level includes free payroll for the firm's own staff, free client setup and marketing resources; co-branding is on the Elite level only. OnPay offers "discounts or revenue sharing", and its FAQ says partners can have OnPay bill clients or bill clients themselves.
Intuit's payroll page for accountants offers three billing options. Bill the firm, and ProAdvisors save 30% for as long as the client subscribes. Bill the client, and the client saves 30% for its first 12 months. Or take a revenue share of 30% of the subscription price; Intuit's banner on the same page describes that as up to 30% for 12 months. The page also says a firm can now split the bill with its client.
We list partner terms only where we have read them at the vendor's own page: OnPay and Intuit. ADP and Paychex price on quote, so any firm pricing would be agreed with their sales teams. Get any partner terms in writing before you quote a client a payroll fee.
Which payroll software syncs with your clients' accounting software?
The payroll product a firm can run most efficiently is usually the one that posts to the ledger it already keeps for that client. Here is each US payroll provider's accounting integration as our data records it; check the client's own accounting software against this column before choosing.
| Provider | Accounting integration |
|---|
| ADP | QuickBooks, Xero, more |
| Gusto | QuickBooks, Xero |
| Homebase | QuickBooks |
| OnPay | QuickBooks, Xero |
| Patriot Software | QuickBooks, Patriot |
| Paychex | QuickBooks, Xero, Sage |
| QuickBooks Payroll | QuickBooks (native) |
| Rippling | QuickBooks, Xero, more |
"Native" at QuickBooks means payroll lives inside QuickBooks Online itself, so there is no sync to break. "Patriot" in Patriot Software's row is its own accounting product, which a firm can use for clients who need both. "More" means the vendor lists further integrations beyond those named.
For a firm with a mixed client book, this column can matter as much as the price. A QuickBooks Online client and a Xero client can sit on the same payroll product only where both appear in its row; otherwise you post journal entries by hand, every pay period, for every client.
Year-end W-2 and 1099 filing for client businesses
At year end a payroll provider should produce and file each client's W-2s for employees and 1099-NEC forms for contractors. OnPay, QuickBooks Payroll and Homebase file both; Patriot files them on Full Service, and on Basic your firm files. The federal dates are the same for every client, and the IRS e-file rule depends on how many forms a client files in total, so a client with a handful of employees and a few contractors can be over it.
For 2026 wages, the IRS General Instructions for Forms W-2 and W-3 (2026) give February 1, 2027 as the date to furnish W-2s to employees and to file Copy A with the Social Security Administration. The Instructions for Forms 1099-MISC and 1099-NEC set January 31 for filing Form 1099-NEC, moving a date that falls on a weekend to the next business day; January 31, 2027 is a Sunday, so 1099-NECs for 2026 payments are also due February 1, 2027. Under the same W-2 instructions, a business that files at least 10 information returns in total, counting W-2s and 1099s together, must e-file them all; the IRS explains the rule on its e-file information returns page.
How each US payroll provider we list handles the forms, with our wording intact:
| Provider | W-2 and 1099 filing |
|---|
| ADP | Yes |
| Deel | Yes |
| Gusto | Yes |
| Homebase | Yes |
| OnPay | Yes |
| Papaya Global | Not stated |
| Patriot Software | Yes |
| Paychex | Yes |
| Payoneer Workforce Management | Not stated |
| QuickBooks Payroll | Yes |
| Remote | 1099 only |
| Rippling | Yes |
"Not stated" means the vendor does not publish it, not that it cannot. "1099 only" at Remote means its US product files contractors' forms but not W-2s in our data.
Through the year, the quarterly federal return is Form 941. If someone other than the client is to sign and file it, the client grants that authority; the IRS form a business uses to authorize a reporting agent to sign and file certain returns, make deposits and receive copies of notices is Form 8655. Confirm at setup whether the payroll provider, your firm or the client holds that role for each return, so a client never ends up with two parties filing, or none.
Payroll providers we left out for accounting firms, and why
The other payroll providers we list are not picks for a firm running domestic client payroll. Each is in the full payroll comparison, and each has a reason:
- Deel, Remote, Papaya Global and Payoneer Workforce Management are built for businesses that hire across borders. Payoneer Workforce Management's US filing is No (EOR only) in our data, and the W-2 and 1099 table above shows where the others stop. For a client that hires abroad, our payroll software for contractors guide compares them.
- ADP and Paychex price on quote and sign clients to a contract our data records as Annual at ADP and Annual at Paychex, so the table cannot cost them for a client and you cannot compare them before a sales call.
- Rippling sells payroll as a module of an HR and IT platform, aimed at growing businesses heading for mid-market; a small client that needs only payroll will not use the rest of the platform.
- Gusto offers full-service filing, but multi-state payroll starts on its Plus plan, above the plan our table costs, and we have not read its accountant terms at source, so we cannot set them beside the picks.
Which payroll software suits your firm?
Pick by the firm you run and the clients you have:
- You want payroll to be a service line with its own margin: OnPay, because one plan fits every client and its program discount rises with your client count, with a revenue share as the alternative.
- Most of your clients' books are in QuickBooks Online: QuickBooks Payroll, because each pay run lands in the ledger you already reconcile.
- Your firm already prepares clients' payroll returns and wants to keep that work: Patriot Software on its Basic tier, moving a client to Full Service when you would rather Patriot file.
- The client runs a restaurant, a shop or other shift-based staff: Homebase, because the schedule and time clock feed the pay run.
For an S corp client, the IRS says on its S corporation compensation page that a shareholder-employee must be paid reasonable compensation for services before non-wage distributions, so even a one-person S corp usually needs a payroll; our guide to payroll software for S corps covers that case.
If one product does not fit every client, a second for the exceptions is reasonable, but each extra payroll system is another set of logins, deadlines and support lines for your staff to learn.