Payroll software handles tax calculations, withholding, filing, and compliance so you don’t have to. It’s essential for S-Corp owners and any business with employees.
Quick answer: Gusto is best overall for features and ease of use. Square Payroll is best value for small teams. Wave is cheapest for businesses in supported states. Most small businesses should budget $40–$80/month for payroll.
Best Payroll Software Compared
| Software | Base Price | Per Employee | Tax Filing | Best For |
|---|---|---|---|---|
| Gusto | $40/mo | $6/mo | All states | Best overall |
| Square Payroll | $35/mo | $6/mo | All states | Small teams |
| Wave Payroll | $20/mo | $6/mo | 14 states full-service | Cheapest option |
| QuickBooks Payroll | $50/mo | $6/mo | All states | QuickBooks users |
| ADP Run | $59/mo | $4/mo | All states | Growing businesses |
| Paychex Flex | Custom | Custom | All states | Complex needs |
| OnPay | $40/mo | $6/mo | All states | Simple pricing |
| Patriot Payroll | $17/mo | $4/mo | All states | Budget full-service |
What Payroll Software Does
| Feature | What It Handles |
|---|---|
| Tax calculations | Federal, state, and local tax withholding |
| Direct deposit | Pays employees electronically |
| Tax filing | Files 941, 940, W-2, state returns |
| Compliance | Handles new hire reporting, ACA tracking |
| Benefits administration | Health insurance, retirement plan deductions |
| Workers’ comp | Integration with insurance providers |
| Time tracking | Some include built-in time tracking |
Payroll Costs by Business Size
| Employees | Gusto | Square | Wave | QuickBooks |
|---|---|---|---|---|
| Just owner (S-Corp) | $46/mo | $41/mo | $26/mo | $56/mo |
| 1–3 employees | $58–$78/mo | $53–$71/mo | $38–$56/mo | $68–$86/mo |
| 5 employees | $70/mo | $65/mo | $50/mo | $80/mo |
| 10 employees | $100/mo | $95/mo | $80/mo | $110/mo |
| 25 employees | $190/mo | $185/mo | $170/mo | $200/mo |
Choosing the Right Payroll Software
| Business Type | Recommended | Why |
|---|---|---|
| Solo S-Corp owner | Square Payroll or Wave | Cheapest, handles single payroll |
| Freelancer with contractors | Gusto | Easy 1099 filing + optional W-2 |
| Small team (1–10) | Gusto | Best balance of features and price |
| Restaurant/retail | Square Payroll | Integrates with Square POS, tip tracking |
| Already using QuickBooks | QuickBooks Payroll | Seamless integration |
| Growing business (10+) | ADP or Paychex | Scalable, HR features |
Payroll Schedule Options
| Frequency | When Paid | Common For |
|---|---|---|
| Weekly | Every week | Hourly/manual labor |
| Biweekly | Every two weeks | Most common overall |
| Semi-monthly | 1st and 15th | Salaried employees |
| Monthly | Once per month | Executives, small businesses |
Bottom Line
Every S-Corp needs payroll software, and it’s worth the $40–$80/month cost to avoid IRS penalties and compliance headaches. Gusto is the best all-around choice for small businesses. Square Payroll and Wave are great budget options. Don’t try to run payroll manually — the risk isn’t worth the savings.
For more, see LLC vs S-Corp, how to pay yourself as a business owner, and best accounting software.