Payroll software calculates wages and withholding, pays employees, and (on most full-service plans) files and pays payroll taxes for you. The differences show up in the details: how many states you need, how fast direct deposit is, whether time tracking and HR tools are included, and how cleanly payroll lands in your books.
Each service below was checked on the vendor's own website in September 2026. Plan names and bundles change often, so confirm the current details before you sign up. Where a vendor publishes a starting price, we show it with the date we saw it.
Payroll is also one of the easiest places for books to go wrong. If you want help keeping payroll records straight in QuickBooks Online, see our lists of bookkeeping services for small businesses in Boise and QuickBooks ProAdvisors in Boise. Churches have their own payroll rules; see our church payroll page.
How we chose
- Sold to US small businesses in September 2026, confirmed on the vendor's own site
- Calculates, files and pays federal, state and local payroll taxes on at least one plan
- Handles both W-2 employees and 1099 contractors
- Connects to common accounting software or includes it
- Publishes what each plan includes, even if pricing is by quote
Gusto
Gusto lists four plans: Contractor Only, Simple, Plus and Premium. Simple covers single-state payroll with unlimited payroll runs and tax filings and payments; it starts at $49/month plus $6 per person as listed on September 23, 2026. Plus adds multi-state payroll, next-day pay and time tracking.
Gusto syncs payroll journal entries to QuickBooks Online and lets you map payroll to your own chart of accounts. It also offers a separate Gusto Solo plan for owners paying themselves through an S corporation.
- Unlimited payroll runs and tax filings on every employee plan
- Contractor Only plan with Form 1099 creation and filing
- Multi-state payroll and next-day pay on Plus
- QuickBooks Online integration that maps to your chart of accounts
Worth knowing
- The Simple plan is single-state; multi-state payroll needs Plus or Premium
- Same-day and instant pay are paid extras below the Premium plan
QuickBooks Payroll
Intuit sells payroll bundled with QuickBooks Online. Its payroll pricing page lists three bundles, each with full-service payroll, auto payroll, 1099 e-filing and tax penalty protection, and says Intuit will calculate, file and pay your payroll taxes.
The entry bundle includes next-day direct deposit; the two higher bundles include same-day direct deposit. Time tracking and HR and hiring tools are in the top bundle.
- Payroll and accounting in the same system
- Payroll taxes calculated, filed and paid for you
- Next-day or same-day direct deposit depending on bundle
- Tax penalty protection on every bundle
Worth knowing
- Bundled with a QuickBooks Online plan, so it suits businesses committed to QuickBooks
- Time tracking is only in the top bundle
OnPay
OnPay's Payroll Essentials plan starts at $49/month plus $6 per worker as listed on September 23, 2026. It covers W-2 and 1099 workers, unlimited pay runs, federal, state and local tax filings and payments, year-end W-2s and 1099s, and multi-state payroll in all 50 states.
HR tools and time tracking are optional add-ons or bundles. OnPay lists integrations with QuickBooks and Xero, and names churches, nonprofits, farms and restaurants among the industries it serves.
- Multi-state payroll included at no extra cost
- Year-end W-2 and 1099 filings included
- QuickBooks and Xero integrations
- First month free, as listed on the pricing page
Worth knowing
- HR and time tracking cost extra
- Church payroll has clergy-specific rules; ask OnPay how it handles your situation
RUN Powered by ADP
RUN is ADP's payroll product for businesses with 1 to 49 employees. It comes in four packages, from Essential Payroll through HR Pro Payroll & HR, with more HR support at each step.
ADP says RUN automatically deducts and files federal, state and local taxes and creates and e-files W-2s and 1099s. It includes a mobile app and connects to accounting software and other business tools.
- Four packages that add HR support as you grow
- Tax filing and W-2/1099 e-filing
- Mobile app for running payroll
- Integrations with accounting software and POS systems
Worth knowing
- Pricing isn't published; you request a quote
- Compare what each package includes, since HR features vary by package
Paychex Flex
Paychex Flex comes in Select, Pro and Enterprise packages. Paychex says it automatically calculates, pays and files payroll taxes, and every package includes mobile access, a payroll dashboard and an employee self-service portal.
The Pro package lists optional assigned specialist support, which suits owners who would rather call a person than work through payroll alone.
- Automatic payroll tax calculation, payment and filing
- Employee self-service portal
- Optional assigned specialist on Pro
- Packages that scale up to larger businesses
Worth knowing
- Pricing isn't published; you request a quote
- The top package is aimed at larger businesses
Patriot Payroll
Patriot offers Basic Payroll and Full Service Payroll. Basic runs payroll and produces tax reports, but you file and deposit the taxes yourself. Full Service adds federal, state and local tax filings and deposits, plus year-end 940, 941, W-2 and W-3 filings at no extra cost.
Both plans include unlimited payroll runs and employee and contractor portals, and they integrate with Patriot's accounting software.
- Choice of do-it-yourself tax filing or full service
- Unlimited payroll runs
- Employee and contractor portals
- 30-day free trial listed on the pricing page
Worth knowing
- On Basic Payroll, filing and paying taxes is your job
- Each additional state is an extra monthly charge on Full Service
Square Payroll
Square Payroll has a Full-Service plan and a Contractor-Only plan. Full-Service starts at $35/month plus $6 per person paid as listed on September 23, 2026, and includes unlimited pay runs, automated federal and state tax payments and filings, and multistate payroll.
Both plans can import timecards from Square point of sale and pay by check, direct deposit or Cash App.
- Timecard import from Square POS
- Automated tax payments and filings on Full-Service
- Contractor-only option
- No long-term contract
Worth knowing
- Most useful if your business already runs on Square
- Support hours are weekdays, Pacific time
Rippling
Rippling Payroll calculates federal, state and local payroll taxes and files them with the right agencies. It is built on the same platform as Rippling's HR tools, so new hires and pay changes flow into payroll without re-entry.
Rippling also supports paying employees and contractors in multiple countries, which is more than most small businesses need but useful if you hire abroad.
- Payroll taxes calculated and filed
- HR data flows straight into payroll
- Global payroll for employees and contractors
- Free account creation
Worth knowing
- Pricing isn't published; you request a demo
- More platform than a very small business may need
How to choose
- Decide who files the taxes. Full-service plans file and pay payroll taxes for you; do-it-yourself plans leave that to you.
- Count your states. Some entry plans cover one state only.
- Check direct deposit timing. Next-day or same-day deposit can be an extra on lower tiers.
- Look at the accounting sync. Payroll should post to the right expense and liability accounts in your books, not as one lump sum.
- Get quotes for quote-only providers so you can compare on the same basis.
Keeping payroll right in your books
Payroll software handles the paychecks, but your books still need to show wages, employer taxes and liabilities correctly. When the payroll sync is mapped badly, the payroll liability accounts stop matching what was actually paid, and that is a common reason owners end up needing catch-up and QuickBooks cleanup.
Danielson Bookkeeping keeps payroll records straight in QuickBooks Online as part of small business bookkeeping, and handles church payroll processing and records for churches, including board-designated housing allowances coordinated with the church's tax adviser. See church payroll for details.
