The short answer
Square Payroll costs $35 a month plus $6 per person and imports time cards and tips from Square POS. Paychex Flex publishes Flex Essentials at $39 a month plus $5 per employee for businesses with fewer than 20 employees and quotes its Basic to Complete packages.
LeadChange Score: editorial assessment based on public information.
Square Payroll wins 1Paychex Flex wins 31 tie
| Dimension | Square Payroll | Paychex Flex |
|---|---|---|
| PricingSquare lists $35 a month plus $6 per person; Paychex Flex Essentials lists $39 plus $5 for businesses under 20 employees, with W-2s and 1099s at extra cost. For 10 employees that is $95 with Square and $89 with Paychex before year-end forms. | $35/mo + $6/employee/mo | $39/mo + $5/employee/mo |
| CapabilitiesBoth run unlimited payrolls with tax filing and pay contractors. Paychex Flex adds HR, benefits and workers' comp modules and higher packages with applicant tracking and learning management; Square adds tip import and free Square Shifts scheduling. 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 | 3 of 12 core capabilities | 12 of 12 core capabilities |
| IntegrationsPaychex Flex connects to QuickBooks, Sage Intacct, Xero, NetSuite, 7shifts and When I Work, with a REST API and webhooks. Square Payroll connects to Square POS, the Square Team App and QuickBooks Online. Intuit QuickBooks, Sage Intacct, Xero, Oracle NetSuite, Jirav, Connecteam, SwyftOps, When I Work, Mindbody, 7shifts, Employee Navigator, BambooHR, Clover, Instant Financial, goHappy | 1 documented | 15 documented |
| Fit and supportPaychex Flex serves small and mid-size businesses with 24/7 payroll support. Square serves small businesses, with payroll specialists on weekdays from 6 a.m. to 6 p.m. PT. Small businesses, mid-market companies | Small businesses | Small businesses, mid-market companies |
| SecuritySquare Payroll states SOC 2 Type II and ISO 27001. Paychex Flex names no security certification on the pages we reviewed. Yes | SOC 2, ISO 27001 | None verified |
| Attribute | Square Payroll | Paychex Flex |
|---|---|---|
| Price transparency | Published | Partly published |
| Best for | Small businesses | Small businesses, mid-market companies |
| Mobile apps | Square Team App | Paychex Flex app (iOS), Paychex Flex app (Android), Paychex Flex Time Kiosk app |
| Support channels | Phone, chat | Phone, chat, email, in-platform help center |
| Founded | 2009 | 1971 |
| Headquarters | Oakland, California, US | Rochester, New York and Cincinnati, Ohio, US (dual headquarters) |
| Attribute | Square Payroll | Paychex Flex |
|---|---|---|
| Pricing model | Base fee + per employee | Base fee + per employee |
| Automatic tax filing | ||
| Contractor payments | ||
| Ownership | Publicly traded | Publicly traded |
Pricing. Square lists $35 a month plus $6 per person; Paychex Flex Essentials lists $39 plus $5 for businesses under 20 employees, with W-2s and 1099s at extra cost. For 10 employees that is $95 with Square and $89 with Paychex before year-end forms.
Capabilities. Both run unlimited payrolls with tax filing and pay contractors. Paychex Flex adds HR, benefits and workers' comp modules and higher packages with applicant tracking and learning management; Square adds tip import and free Square Shifts scheduling.
Integrations. Paychex Flex connects to QuickBooks, Sage Intacct, Xero, NetSuite, 7shifts and When I Work, with a REST API and webhooks. Square Payroll connects to Square POS, the Square Team App and QuickBooks Online.
Fit and support. Paychex Flex serves small and mid-size businesses with 24/7 payroll support. Square serves small businesses, with payroll specialists on weekdays from 6 a.m. to 6 p.m. PT.
Security. Square Payroll states SOC 2 Type II and ISO 27001. 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
At 10 employees, Paychex Flex Essentials lists less: $89 a month against Square’s $95. Paychex then bills W-2s and 1099s and may add tax administration fees, while Square only charges $3 per paper form mailed if you opt in. From 20 employees, Paychex prices by quote.
Square offers health insurance through SimplyInsured, where the employer pays at least half the premiums; it is not offered in HI, MN, ND, SD, VT or DC. Paychex Flex sells group health insurance and 401(k) plans as add-ons, and every package includes Paychex Flex Perks, an employee perks marketplace.
Paychex offers 24/7 payroll support by phone, chat and email. Square’s payroll specialists take calls and chats Monday to Friday, 6 a.m. to 6 p.m. PT.
Paychex Promise lets you delay the payroll debit by up to 7 days; it is free for the first 3 months and then costs $99 a year. Square Payroll offers employees early pay to a debit card for 1.75% of net pay, free with Cash App.
Yes. Square’s contractor-only plan costs $6 per contractor a month, with no base fee, and pays by direct deposit, check or Cash App. Paychex Flex handles 1099 contractor reporting and payments in its payroll.
Paychex’s online setup is self-guided, and a first payroll can run as soon as the same day. Square Payroll charges no setup fee and bills monthly with no long-term contract.
Only Square Payroll states SOC 2 Type II and ISO 27001.
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