The short answer
OnPay costs $49 a month plus $6 per worker, with tax filings, W-2s, 1099s and multi-state payroll included. Paychex Flex publishes one entry plan, Flex Essentials at $39 a month plus $5 per employee for businesses with fewer than 20 workers, where W-2s and 1099s cost extra; its Basic to Complete packages are quoted.
LeadChange Score: editorial assessment based on public information.
OnPay wins 1Paychex Flex wins 21 tie
| Dimension | OnPay | Paychex Flex |
|---|---|---|
| PricingPaychex Flex Essentials lists $39 a month plus $5 per employee for under 20 workers, with W-2s and 1099s at additional cost; other packages are quoted. OnPay lists $49 plus $6 with year-end forms and multi-state payroll included. | $49/mo + $6/employee/mo (Payroll Essentials plan) | $39/mo + $5/employee/mo |
| CapabilitiesBoth run unlimited payrolls with tax filings and pay contractors. Paychex Flex adds garnishment payments, applicant tracking, learning management and SUI service in higher packages; OnPay adds HR, time tracking and benefits administration as add-ons. Run payroll in as little as 30 seconds, Unlimited payroll processing, Automated payroll tax calculation, filing and payment (Taxpay), Multi-state payroll tax compliance, Paychex Pre-check employee paycheck review, Intelligent Pay Cycle error flagging, 1099 contractor reporting and payments, Paychex Flex mobile app | 10 of 12 core capabilities | 12 of 12 core capabilities |
| IntegrationsPaychex Flex connects to QuickBooks, Sage Intacct, Xero, NetSuite and scheduling apps such as When I Work and 7shifts, with a REST API and webhooks. OnPay lists 9 integrations, including QuickBooks Online and Xero. Intuit QuickBooks, Sage Intacct, Xero, Oracle NetSuite, Jirav, Connecteam, SwyftOps, When I Work, Mindbody, 7shifts, Employee Navigator, BambooHR, Clover, Instant Financial, goHappy | 9 native | 15 documented |
| SecurityOnPay states SOC 2 Type II. Paychex Flex names no security certification on the pages we reviewed. Yes | SOC 2 | None verified |
| Attribute | OnPay | Paychex Flex |
|---|---|---|
| Price transparency | Published | Partly published |
| Support channels | Phone, email, chat | Phone, chat, email, in-platform help center |
| Founded | 2011 | 1971 |
| Headquarters | Atlanta, Georgia | Rochester, New York and Cincinnati, Ohio, US (dual headquarters) |
| Ownership | Private | Publicly traded |
| Attribute | OnPay | Paychex Flex |
|---|---|---|
| Pricing model | Base fee + per employee | Base fee + per employee |
| Best for | Small businesses, mid-market companies | Small businesses, mid-market companies |
| Automatic tax filing | ||
| Contractor payments |
| Employees | OnPay Payroll Essentials | Paychex Flex Essentials |
|---|---|---|
| 10 | $109/mo | $89/mo (lowest) |
| 50 | $349/mo | $289/mo (lowest) |
| 200 | $1,249/mo | $1,039/mo (lowest) |
Monthly list price of each product’s entry plan with published per-employee pricing.
Pricing. Paychex Flex Essentials lists $39 a month plus $5 per employee for under 20 workers, with W-2s and 1099s at additional cost; other packages are quoted. OnPay lists $49 plus $6 with year-end forms and multi-state payroll included.
Capabilities. Both run unlimited payrolls with tax filings and pay contractors. Paychex Flex adds garnishment payments, applicant tracking, learning management and SUI service in higher packages; OnPay adds HR, time tracking and benefits administration as add-ons.
Integrations. Paychex Flex connects to QuickBooks, Sage Intacct, Xero, NetSuite and scheduling apps such as When I Work and 7shifts, with a REST API and webhooks. OnPay lists 9 integrations, including QuickBooks Online and Xero.
Fit and support. Paychex Flex offers 24/7 payroll support by phone, chat and email. OnPay answers by phone from 9 a.m. to 8 p.m. ET on weekdays.
Security. OnPay states SOC 2 Type II. Paychex Flex names no security certification on the pages we reviewed.
Patriot Payroll has the highest LeadChange Score in Payroll Software after excluding these two (9.3/10).
From $17/mo + $4/employee/mo
OnPay charges $49 a month plus $6 per worker, $109 for 10, W-2s and 1099s included. Paychex Flex Essentials charges $39 plus $5, $89 for 10 workers, plus W-2 and 1099 fees and possible tax administration fees; larger businesses get a quote.
Paychex Flex offers 24/7 payroll support and an in-platform help center. OnPay’s phone line is open 9 a.m. to 8 p.m. ET, Monday to Friday, with email and chat as well.
Yes. OnPay serves small and mid-size businesses at the same price per worker: 50 workers cost $349 a month. Paychex’s published Flex Essentials price is only for businesses with fewer than 20 employees; above that, Paychex quotes.
Paychex Promise, which delays the payroll debit up to 7 days, is free for 3 months and then $99 a year; W-2s and 1099s cost extra on Flex Essentials, and add-ons such as time and attendance are quoted. OnPay publishes its add-ons: HR for $15 a month plus $2 per worker and time tracking for $15 plus $4.
OnPay sells three discounted bundles: payroll with time tracking and HR for $70 a month plus $10 per worker, payroll with HR, compliance resources and live HR support for $120 plus $7, and all of it for $130 plus $10. Paychex Flex sells Basic, Foundations, Advanced and Complete by quote, adding garnishment services, handbooks, applicant tracking and a payroll specialist as you move up.
Paychex Flex connects to QuickBooks, Sage Intacct, Xero and Oracle NetSuite, and to scheduling apps such as When I Work and 7shifts. OnPay connects to QuickBooks Online and Xero, plus JazzHR for hiring and TurboTax.
Only OnPay states SOC 2 Type II.
OnPay ranks #5 of 12 in our payroll software ranking. Besides Paychex Flex, the highest-scored are Patriot Payroll, QuickBooks Payroll, and Gusto. Every alternative, matched to the reason you might switch: OnPay alternatives.
Your team size, what matters most and your role: see which one fits more of your answers, from verified facts and list prices. Then, if you like, ask to hear from both.
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What the LeadChange Score means
A 0–10 editorial assessment built only from verified facts, across six weighted dimensions: capabilities, pricing, integrations, security, fit and support, and data confidence.
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