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Paychex Flex vs QuickBooks Payroll: $64 plus unpublished fees against $85 in full
Updated Oct 6, 2026
Paychex Flex Essentials costs $39 a month plus $5 per employee, $64 for five, but tax administration "Additional fees may apply" and W-2s and 1099s cost extra, amounts not published. QuickBooks Workforce Payroll costs $50 plus $7 per employee, $85 for five, and publishes its state and contractor fees, such as $12 a month per additional state. Paychex files "identified local" taxes; Workforce Payroll files none. QuickBooks includes next-day direct deposit.
At a glance, by our score
- Lowest price
#4 Paychex Flex
Teams under 20 employees that sign up online from $64 a month for five, with tax filing billed extra
8.3/10Very goodOur scoreVisit Paychex FlexOn paychex.com #6 QuickBooks Payroll
QuickBooks Online users who want federal and state payroll taxes filed from $85 a month for five
6.7/10FairOur scoreVisit QuickBooks PayrollOn quickbooks.intuit.com
Paychex Flex's lowest monthly price is lower than QuickBooks Payroll's, checked Sep 27, 2026 and Sep 27, 2026.
Side by side
| Criterion | Paychex Flex | QuickBooks Payroll |
|---|---|---|
| Overall score | 8.3/10Very goodOur score #4 of 7 | 6.7/10FairOur score #6 of 7 |
| Cost for five employees (35%) | 9.3 / 10 | 8.2 / 10 |
| Included on the entry plan (20%) | 10.0 / 10 | 8.0 / 10 |
| Tax filing (20%) | 10.0 / 10 | 6.0 / 10 |
| Tax accuracy guarantee (10%) | 0.0 / 10 | 0.0 / 10 |
| Support (10%) | 10.0 / 10 | 10.0 / 10 |
| Free trial (5%) | 0.0 / 10 | 0.0 / 10 |
| Price from | $5 / month | $7 / month |
| Best for | Teams under 20 employees that sign up online from $64 a month for five, with tax filing billed extra | QuickBooks Online users who want federal and state payroll taxes filed from $85 a month for five |
| Visit | Visit Paychex FlexOn paychex.com | Visit QuickBooks PayrollOn quickbooks.intuit.com |
Who should pick which
- Paychex Flex: Teams under 20 employees that sign up online from $64 a month for five, with tax filing billed extra
- QuickBooks Payroll: QuickBooks Online users who want federal and state payroll taxes filed from $85 a month for five
At a glance
| Paychex Flex | QuickBooks Payroll | |
|---|---|---|
| Entry plan and billing | Paychex Flex Essentials: $39 a month + $5 per employee, under 20 employees | Workforce Payroll: $50 a month + $7 per employee, monthly only |
| Cost for five employees | $64 a month, before tax-filing and W-2/1099 fees it doesn't publish | $85 a month |
| Tax filing | Federal, state and "identified local"; "Additional fees may apply" | Federal and state, one state included (each extra $12 a month); no local taxes (disclosures) |
| Included on the entry plan | Unlimited runs, direct deposit, employee self-service, contractor 1099s (extra cost), new-hire reporting | Unlimited runs, direct deposit, employee portal, 1099 e-file; new-hire filing read as Premium and Elite only |
| Tax penalty guarantee | Its pages don't say | Elite only, up to $25,000 a year |
| Support | "24/7 support options"; live chat or phone (support page) | Phone and chat in business hours |
| Free trial | No; no cost until your first payroll | None on the pricing page; 50% off the base fee for 3 months |
Prices and features from Paychex Flex's pricing page and QuickBooks Payroll's pricing page, read Sep 27, 2026.
Price
One employee costs $44 a month on Paychex Flex Essentials and $57 on QuickBooks Workforce Payroll. Five cost $64 and $85, a $21 gap on published prices.
The Paychex price is a floor. Its Essentials page says payroll tax administration "*Additional fees may apply" and W-2s and 1099s are "**Available at additional cost"; you see those fees when you sign the service agreement. QuickBooks publishes its extras on its disclosures page: $12 a month for each state after the first and $7 a month on Workforce Payroll for contractor direct deposit, "per contractor payment".
QuickBooks shows 50% off the monthly base price for 3 months ($25 instead of $50) for new monthly customers; per-employee and state fees stay full, so five cost $60 a month for those months. No end date is given. Paychex shows no introductory price and charges nothing until your first payroll.
Where they differ
- Local taxes. Paychex files federal, state and "identified local" payroll taxes. QuickBooks says "QuickBooks Workforce Payroll does not offer local tax payments and filings"; certain local taxes are on Premium and Elite only.
- Pay speed. Workforce Payroll includes next-day direct deposit if you run payroll by 5:00 PM (pricing page). Paychex's pages don't say whether Essentials offers next-day deposits.
- New-hire reporting. Paychex Essentials includes new-hire reporting. Intuit's pages conflict on Workforce Payroll; we use the worse reading, Premium and Elite only.
- Penalty guarantee. Paychex's pages don't say it pays penalties from its own errors. QuickBooks' penalty protection, up to $25,000 a year, is on Elite only ($134 + $17 per employee).
- Support. Paychex says "24/7 support options available", with live chat or a call (support page). QuickBooks has phone and chat in business hours; weekend support is on Premium and Elite.
Paychex Flex Essentials is for businesses with fewer than 20 employees and/or contractors; its larger packages are quote-only. Paychex names no extra fee for employees in other states.
Who should pick which
Pick Paychex Flex if you have local payroll taxes, want support around the clock or new-hire reports on the entry plan, and will get the extra fees in writing before you sign.
Pick QuickBooks Payroll if you want the state and contractor fees published up front, need next-day direct deposit, have no local taxes, or want payroll from the company that sells QuickBooks Online.
Both appear in our payroll services ranking and our list for construction and trades. Scoring is on the methodology page.