Payroll is one of those things you just need to work — accurately, on time, and without you having to think about it. For a small business with 1-10 employees, you don’t need enterprise HR software. You need something that calculates pay, files taxes, handles direct deposit, and doesn’t cost a fortune.
We compared the top payroll options for micro-businesses on price, ease of use, tax filing, and how much of the process they actually automate.
Quick Comparison
| Software | Best For | Base Price | Per Employee | Auto Tax Filing | Integrated Accounting |
|---|---|---|---|---|---|
| Gusto | Best overall experience | $40/mo | $6/mo | Yes (all 50 states) | Yes (QuickBooks, Xero, FreshBooks) |
| OnPay | Best for niche industries (churches, farms, nonprofits) | $36/mo | $6/mo | Yes (all 50 states) | Yes (QuickBooks, Xero, Aplos) |
| Patriot | Best budget option | $17/mo | $4/mo | Yes (Full Service) | Yes (Patriot Accounting) |
| QuickBooks Payroll | Best for QuickBooks users | $45/mo | $5/mo | Yes | Yes (native) |
| ADP Run | Best if you might grow beyond 10 employees | $59/mo | $4/mo | Yes | Partial |
| Square Payroll | Best for hourly/shift workers | $29/mo + $5/employee | Included | Yes | Partial |
1. Gusto — Best Overall
Gusto is the payroll platform that small business owners actually enjoy using. The interface is clean, onboarding new hires takes minutes, and tax filings happen automatically. If you want payroll to be something you barely think about, Gusto is the answer.
Pros:
- Easiest setup and daily use of any payroll platform
- Automatic tax filing in all 50 states
- Employee self-service portal (W-2s, pay stubs, tax documents)
- Built-in time tracking and PTO management
- Benefits administration (health, 401k, 529 plans)
- Strong HR tools on higher tiers
- Excellent onboarding experience for new hires
- Integrates with QuickBooks, Xero, FreshBooks
Cons:
- Base price is higher than Patriot
- HR features cost extra on Plus and Premium
- Customer support can be slow during Q1 tax season
- No built-in accounting — relies on integrations
- International contractors require Gusto Global (separate product)
Pricing: Simple $40/mo + $6/employee; Plus $60/mo + $9/employee; Premium $80/mo + $12/employee
Best for: Small businesses that want the smoothest payroll experience and don’t mind paying a bit more for it.
2. Patriot Software — Best Budget Option
Patriot offers the lowest entry price of any full-service payroll platform. If your business has 2-5 employees and every dollar matters, Patriot handles the essentials well without the premium price tag.
Pros:
- Lowest base price of any full-service payroll
- Simple, straightforward interface
- Free direct deposit
- Integrated accounting available (Patriot Accounting, $12/mo)
- Free tax filing in all 50 states (Full Service plan)
- Good customer support
- Free 30-day trial
- Simple pricing — no hidden fees
Cons:
- Interface is basic compared to Gusto
- Limited HR and benefits features
- Fewer integrations than competitors
- No built-in time tracking (add-on available)
- Reporting is minimal
- No international payroll
Pricing: Basic $17/mo + $4/employee (self-service tax filing); Full Service $37/mo + $4/employee (auto tax filing)
Best for: Small businesses with tight budgets that need payroll done right without paying for features they don’t use.
3. OnPay — Best for Niche Industries
OnPay handles payroll for standard small businesses perfectly well, but it stands out for niche industries: churches (clergy housing allowance), farms (agricultural workers), nonprofits, and restaurants (tipped employees). If your payroll has unusual requirements, OnPay probably handles them natively.
Pros:
- Dedicated products for churches, farms, nonprofits, and restaurants
- Handles complex tax situations that others require manual setup for
- Automatic tax filing in all 50 states
- Free tax penalty protection
- Excellent, US-based customer support
- Integrates with QuickBooks, Xero, and Aplos
- Workers’ comp and benefits administration
- Custom payroll reports
Cons:
- Slightly higher base price than Gusto
- Interface is less polished than Gusto
- HR features less comprehensive than ADP
- Fewer integrations than Gusto or QuickBooks
- No free plan or trial (demo available)
Pricing: $36/mo + $6/employee (includes tax filing)
Best for: Businesses with industry-specific payroll needs — churches with clergy, farms with seasonal workers, restaurants with tipped staff — that don’t want to manually configure special tax treatment.
4. QuickBooks Payroll — Best for QuickBooks Users
If your business already runs on QuickBooks Online, adding QuickBooks Payroll keeps everything in one system. Same login, same chart of accounts, same reports. No syncing, no exports, no separate platforms.
Pros:
- Seamless integration with QuickBooks Online
- Same-day direct deposit available
- Automatic tax filing and payments
- Employee self-service portal
- Health benefits and 401(k) options
- Familiar interface for QuickBooks users
- No separate login or data syncing
Cons:
- No free trial
- Pricing has increased significantly (Core now $45/mo)
- Limited time tracking on Core plan
- Customer support quality is inconsistent
- HR features require Premium or Elite
- Doesn’t handle niche industries as well as OnPay
Pricing: Core $45/mo + $5/employee; Premium $75/mo + $8/employee; Elite $125/mo + $10/employee
Best for: Businesses already using QuickBooks for accounting that want payroll in the same system.
5. Square Payroll — Best for Hourly Workers
If your business runs on Square POS and has hourly or shift-based employees, Square Payroll integrates seamlessly. Time tracking from the Square POS flows directly into payroll. No manual entry, no separate time clock system.
Pros:
- Seamless integration with Square POS and time tracking
- Handles hourly, salaried, and contractor payments
- Automatic tax filing
- Workers’ comp built in
- Good for businesses with tipped employees
- Simple, Square-style interface
- No minimum employee count
Cons:
- Only makes sense if you use Square POS
- No built-in accounting integration (except Square)
- Limited benefits administration
- HR features are minimal
- Reporting is basic
- No PTO management on basic plan
Pricing: $29/mo + $5/employee (W-2); $6/mo per contractor (1099)
Best for: Retail, food service, and other businesses using Square POS with hourly employees.
How to Choose
1. Do you already use accounting software?
QuickBooks → QuickBooks Payroll. Patriot Accounting → Patriot. Nothing yet → Gusto.
2. What’s your budget?
Under $30/mo → Patriot. $30-50/mo → Gusto or OnPay. Already paying for QuickBooks? → QuickBooks Payroll.
3. Any special payroll situations?
Clergy → OnPay. Agricultural workers → OnPay. Tipped employees → Square Payroll or OnPay. None → Gusto.
4. How many employees?
1-5 → Any option works. 5-10 → Gusto (scales well). Planning to grow beyond 10 → ADP Run or Gusto.
Our Top Pick
For most small businesses, Gusto is the best combination of easy, complete, and reliable. If budget is the priority, Patriot handles the essentials well at the lowest price. If you have niche payroll needs (churches, farms, restaurants), OnPay handles what others make you configure manually.
SoftDecide helps churches, nonprofits, and small organizations find the right software. Our comparisons are independently researched. We may earn a commission if you purchase through links on this page — at no extra cost to you.
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