Quick Overview
- 1#1: Gusto - Full-service payroll, HR, and benefits platform designed for small businesses and self-employed owners with automated tax filing and direct deposit.
- 2#2: OnPay - Affordable, full-service payroll software offering unlimited payroll runs, expert support, and seamless integrations for solopreneurs and small teams.
- 3#3: QuickBooks Payroll - Integrated payroll solution with QuickBooks accounting that automates taxes, filings, and payments for self-employed professionals.
- 4#4: Wave Payroll - Low-cost payroll add-on to free accounting software, ideal for freelancers and self-employed handling taxes and direct deposits.
- 5#5: Patriot Software - Budget-friendly full-service payroll with direct deposit, tax filing, and 24/7 support tailored for small businesses and independents.
- 6#6: Square Payroll - Simple payroll integrated with Square payments, offering next-day direct deposit and automated tax compliance for self-employed merchants.
- 7#7: ADP RUN - Scalable payroll software powered by ADP for small businesses, featuring automated taxes, compliance, and HR tools.
- 8#8: Rippling - All-in-one platform combining payroll, HR, and IT management with global payroll support for growing self-employed operations.
- 9#9: Paychex Flex - Comprehensive payroll and HR services with expert guidance, time tracking, and benefits administration for small business owners.
- 10#10: SurePayroll - Straightforward payroll software providing tax calculations, filings, and direct deposit at a low cost for self-employed and small teams.
We ranked tools based on key factors including feature depth (automation, direct deposit, tax filing), user experience (ease of use), reliability, and value, ensuring they cater to the diverse needs of self-employed individuals and small operations.
Comparison Table
Managing payroll as a self-employed individual becomes easier with the right tools, and this comparison table breaks down top options like Gusto, OnPay, QuickBooks Payroll, Wave Payroll, Patriot Software, and more. Readers will gain insights into how each solution handles costs, tax filing, user-friendliness, and extra features to identify the best fit for their unique business needs. Whether prioritizing affordability or advanced capabilities, this guide simplifies the process of choosing the ideal software.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Gusto Full-service payroll, HR, and benefits platform designed for small businesses and self-employed owners with automated tax filing and direct deposit. | specialized | 9.4/10 | 9.6/10 | 9.5/10 | 8.9/10 |
| 2 | OnPay Affordable, full-service payroll software offering unlimited payroll runs, expert support, and seamless integrations for solopreneurs and small teams. | specialized | 8.7/10 | 9.2/10 | 8.5/10 | 8.0/10 |
| 3 | QuickBooks Payroll Integrated payroll solution with QuickBooks accounting that automates taxes, filings, and payments for self-employed professionals. | specialized | 8.2/10 | 9.0/10 | 8.0/10 | 7.5/10 |
| 4 | Wave Payroll Low-cost payroll add-on to free accounting software, ideal for freelancers and self-employed handling taxes and direct deposits. | specialized | 8.2/10 | 7.8/10 | 9.3/10 | 9.5/10 |
| 5 | Patriot Software Budget-friendly full-service payroll with direct deposit, tax filing, and 24/7 support tailored for small businesses and independents. | specialized | 8.2/10 | 7.9/10 | 8.6/10 | 9.1/10 |
| 6 | Square Payroll Simple payroll integrated with Square payments, offering next-day direct deposit and automated tax compliance for self-employed merchants. | specialized | 7.8/10 | 8.2/10 | 9.1/10 | 7.0/10 |
| 7 | ADP RUN Scalable payroll software powered by ADP for small businesses, featuring automated taxes, compliance, and HR tools. | enterprise | 7.1/10 | 8.4/10 | 6.7/10 | 5.9/10 |
| 8 | Rippling All-in-one platform combining payroll, HR, and IT management with global payroll support for growing self-employed operations. | enterprise | 4.5/10 | 5.2/10 | 6.8/10 | 2.8/10 |
| 9 | Paychex Flex Comprehensive payroll and HR services with expert guidance, time tracking, and benefits administration for small business owners. | enterprise | 6.2/10 | 7.8/10 | 7.0/10 | 4.8/10 |
| 10 | SurePayroll Straightforward payroll software providing tax calculations, filings, and direct deposit at a low cost for self-employed and small teams. | specialized | 6.8/10 | 6.5/10 | 8.2/10 | 5.9/10 |
Full-service payroll, HR, and benefits platform designed for small businesses and self-employed owners with automated tax filing and direct deposit.
Affordable, full-service payroll software offering unlimited payroll runs, expert support, and seamless integrations for solopreneurs and small teams.
Integrated payroll solution with QuickBooks accounting that automates taxes, filings, and payments for self-employed professionals.
Low-cost payroll add-on to free accounting software, ideal for freelancers and self-employed handling taxes and direct deposits.
Budget-friendly full-service payroll with direct deposit, tax filing, and 24/7 support tailored for small businesses and independents.
Simple payroll integrated with Square payments, offering next-day direct deposit and automated tax compliance for self-employed merchants.
Scalable payroll software powered by ADP for small businesses, featuring automated taxes, compliance, and HR tools.
All-in-one platform combining payroll, HR, and IT management with global payroll support for growing self-employed operations.
Comprehensive payroll and HR services with expert guidance, time tracking, and benefits administration for small business owners.
Straightforward payroll software providing tax calculations, filings, and direct deposit at a low cost for self-employed and small teams.
Gusto
specializedFull-service payroll, HR, and benefits platform designed for small businesses and self-employed owners with automated tax filing and direct deposit.
Full-service tax compliance where Gusto files and pays federal, state, and local taxes automatically.
Gusto is a full-service payroll and HR platform tailored for small businesses and self-employed professionals, automating payroll runs, tax calculations, filings, and payments for both W-2 employees and 1099 contractors. For self-employed users, it excels in managing contractor payments, generating 1099 forms, and ensuring compliance without needing in-house expertise. Its integration with accounting tools and benefits administration makes it a scalable solution as solopreneurs grow.
Pros
- Automated tax filing and payments handled end-to-end
- Intuitive interface with mobile app for on-the-go management
- Robust contractor management including 1099 generation
Cons
- Monthly base fee applies even with low or no payments
- Overkill and pricey for purely solo self-employed without hires
- Limited built-in invoicing or expense tracking for freelancers
Best For
Self-employed professionals and solopreneurs who pay contractors or anticipate hiring, needing compliant payroll without hassle.
Pricing
Contractor-only plan starts at $35/month base + $6/active contractor; full payroll from $40/month + $6/person/month (billed annually for discounts).
OnPay
specializedAffordable, full-service payroll software offering unlimited payroll runs, expert support, and seamless integrations for solopreneurs and small teams.
Guaranteed 100% on-time and accurate payroll tax filings with penalty protection
OnPay is a full-service payroll platform tailored for small businesses and self-employed individuals, offering automated payroll processing, tax calculations, filings, and 1099 contractor payments. It supports unlimited payroll runs at any frequency, multi-state compliance, and seamless integrations with accounting tools like QuickBooks. Ideal for self-employed users managing occasional contractors, it provides expert support and guaranteed accuracy without requiring in-house payroll expertise.
Pros
- Seamless 1099 filing and contractor payments
- Unlimited payroll runs with no extra fees
- 100% accuracy guarantee on tax filings and payments
Cons
- Base monthly fee applies even for low-volume users
- Overkill for purely solo self-employed without contractors
- Initial setup requires some time investment
Best For
Self-employed professionals or solopreneurs who regularly pay contractors and need robust 1099 and compliance tools.
Pricing
$40 base fee per month + $6 per employee or contractor paid (no contracts, month-to-month).
QuickBooks Payroll
specializedIntegrated payroll solution with QuickBooks accounting that automates taxes, filings, and payments for self-employed professionals.
One-click 1099 e-filing and contractor payment tracking integrated directly into QuickBooks
QuickBooks Payroll is an integrated payroll solution from Intuit that automates paycheck processing, tax calculations, withholdings, and filings for small businesses and self-employed users. It supports W-2 employee payments, 1099 contractor filings, and owner draws, with seamless syncing to QuickBooks accounting software. For self-employed individuals, it simplifies paying contractors and tracking payroll expenses within familiar QuickBooks tools.
Pros
- Seamless integration with QuickBooks for unified accounting and payroll
- Automated federal and state tax filings including 1099 e-filing for contractors
- Next-day direct deposit and auto-payroll options reduce manual work
Cons
- Higher cost structure with base fees even for low-volume self-employed use
- Overkill for solo users without employees or contractors
- Requires a QuickBooks Online subscription for full functionality
Best For
Self-employed business owners who pay contractors regularly and want payroll integrated with their QuickBooks accounting.
Pricing
Core plan starts at $45/month + $6 per employee/contractor; Premium $80/month + $9; Elite $125/month + $11 (billed annually for discounts)
Wave Payroll
specializedLow-cost payroll add-on to free accounting software, ideal for freelancers and self-employed handling taxes and direct deposits.
Unlimited free ACH payments to contractors with no monthly fees
Wave Payroll is a cloud-based solution from Wave Apps that integrates seamlessly with their free accounting and invoicing tools, enabling self-employed users to easily pay contractors and handle basic payroll needs. It supports unlimited free ACH payments to independent contractors, automatic 1099 form generation, and tax calculations, making it ideal for solopreneurs without employees. For those hiring employees, it offers full-service payroll with direct deposit and tax filing in select US states and Canada.
Pros
- Free unlimited payments to contractors via ACH
- Seamless integration with Wave's free accounting software
- Automated 1099 filings and simple tax calculations
Cons
- Full employee payroll with tax filing limited to 14 US states and Canada
- Lacks advanced features for complex payroll scenarios
- Customer support primarily self-serve with limited live options
Best For
Self-employed solopreneurs and freelancers who frequently pay independent contractors but rarely hire employees.
Pricing
Free for unlimited contractor payments; employee payroll starts at $20/month base + $6 per employee (full service varies by location).
Patriot Software
specializedBudget-friendly full-service payroll with direct deposit, tax filing, and 24/7 support tailored for small businesses and independents.
In-house, American-based phone support with payroll experts available during business hours
Patriot Software offers straightforward online payroll solutions tailored for small businesses and self-employed individuals, with Basic Payroll for self-managed processing and Full Service Payroll where experts handle tax filings and compliance. It supports direct deposit, automatic tax calculations, new hire reporting, and multi-state payroll, making it suitable for solopreneurs filing their own quarterly taxes. The platform emphasizes affordability and reliability, backed by in-house U.S.-based support.
Pros
- Extremely affordable pricing for solo users
- In-house U.S. customer support with quick response times
- Accuracy guarantee and on-time tax filing assurance
Cons
- Limited integrations with popular accounting tools like QuickBooks
- No built-in invoicing or time tracking for self-employed workflows
- Basic reporting lacks advanced analytics
Best For
Self-employed individuals or micro-businesses seeking simple, low-cost payroll processing without needing extensive features.
Pricing
Basic Payroll: $17/month base + $4/employee; Full Service: $37/month base + $4/employee; 30-day free trial.
Square Payroll
specializedSimple payroll integrated with Square payments, offering next-day direct deposit and automated tax compliance for self-employed merchants.
Deep integration with Square POS for automatic tip pooling and sales-based payroll adjustments
Square Payroll is a user-friendly payroll solution designed for small businesses, enabling self-employed users to pay W-2 employees and 1099 contractors with automated calculations and direct deposits. It integrates seamlessly with Square's POS and other tools, handling payroll runs, tax withholdings, and filings in select states. While versatile for solopreneurs scaling up, it's best suited for those already in the Square ecosystem rather than pure solo operators.
Pros
- Seamless integration with Square POS for effortless sales-to-payroll syncing
- Supports both W-2 employees and 1099 contractors with automated filings
- Quick setup and mobile-friendly interface for on-the-go management
Cons
- Monthly platform fee applies even for low-volume users
- Full automated tax filing limited to 16 states
- Lacks advanced HR tools like benefits administration for growing teams
Best For
Self-employed Square POS users hiring occasional contractors or part-time help who value ecosystem integration over standalone payroll.
Pricing
Core: $35 base + $6/team member or contractor/month; Plus: $85 base + $9/month; Premium: custom quote; no contracts required.
ADP RUN
enterpriseScalable payroll software powered by ADP for small businesses, featuring automated taxes, compliance, and HR tools.
Payroll accuracy guarantee, covering penalties if ADP errors cause tax issues
ADP RUN is a robust payroll platform from ADP designed primarily for small businesses, offering automated payroll processing, tax calculations, filings, and payments for W-2 employees and 1099 contractors. It includes HR tools, benefits administration, and compliance features to handle federal, state, and local regulations. While scalable for growing teams, it's often overkill for purely self-employed users without staff, functioning more as SMB payroll than a lightweight solo solution.
Pros
- Automated tax filing and direct deposits with accuracy guarantees
- Scalable plans that grow with your business
- 24/7 customer support and expert compliance assistance
Cons
- Expensive base fees make it poor value for solo self-employed users
- Steep learning curve and complex interface for beginners
- Limited focus on freelance-specific tools like simple invoicing or expense tracking
Best For
Self-employed business owners who occasionally hire contractors or a small team and prioritize compliance over simplicity.
Pricing
Essential plan starts at $59/month + $4/employee; Enhanced at $99/month + $7/employee; Complete at $148/month + $11/employee (annual billing required for discounts).
Rippling
enterpriseAll-in-one platform combining payroll, HR, and IT management with global payroll support for growing self-employed operations.
Unified HR-payroll-IT platform that automates employee offboarding and device reclamation in one click
Rippling is a comprehensive workforce management platform that unifies HR, payroll, IT, and finance operations, primarily designed for businesses with employees and contractors. It automates payroll processing, tax filings, and payments across 100+ countries, with seamless integrations for device management and benefits administration. For self-employed users, it offers basic contractor payment tools but falls short on solo-specific features like mileage tracking, expense categorization for Schedule C, or automated quarterly tax estimates.
Pros
- Supports contractor payments and global payroll for occasional hires
- Intuitive interface with strong automation for basic payroll runs
- Extensive integrations with accounting and productivity tools
Cons
- Overkill and underutilized for solo self-employed tax management
- High pricing not justified for single-user scenarios
- Complex setup geared toward teams rather than individuals
Best For
Self-employed professionals who hire contractors sporadically and anticipate scaling to a full team.
Pricing
Starts at $8 per user/month for core HR (minimum 1 user), plus $5-11/user/month for payroll add-on and per-transaction fees; custom quotes for advanced features.
Paychex Flex
enterpriseComprehensive payroll and HR services with expert guidance, time tracking, and benefits administration for small business owners.
Full-service payroll tax compliance with guaranteed accuracy and filing
Paychex Flex is a robust cloud-based payroll and HR platform primarily designed for small to medium-sized businesses, offering automated payroll processing, tax filing, compliance management, and employee self-service portals. It handles W-2 payroll, benefits administration, and time tracking, with strong integrations for accounting software. For self-employed users, it provides reliable tax handling but is often overkill and costly for solo operations without employees.
Pros
- Automated federal, state, and local tax filing and payments
- Strong customer support with dedicated specialists
- Integrations with QuickBooks, ADP, and other accounting tools
Cons
- High pricing not suited for solo self-employed users
- Complex setup and features unnecessary for simple needs
- Minimum fees apply even for single-user payroll
Best For
Self-employed individuals or solopreneurs who occasionally hire contractors or a small team and need enterprise-level compliance.
Pricing
Quote-based; typically $59+ base fee per month plus $5 per employee, with additional costs for HR and benefits modules.
SurePayroll
specializedStraightforward payroll software providing tax calculations, filings, and direct deposit at a low cost for self-employed and small teams.
Unlimited payroll runs for a flat employee fee, ideal for frequent small payments
SurePayroll is an online payroll platform tailored for small businesses, providing automated payroll processing, tax calculations, filings, and direct deposit services. It supports W-2 employees and 1099 contractors, with integrations for QuickBooks and other accounting tools. For self-employed users, it offers basic contractor payment and 1099 management but is primarily designed for those with 1+ employees rather than solo operations.
Pros
- User-friendly interface for quick payroll runs
- Automatic federal and state tax filing
- Next-day direct deposit option
Cons
- Monthly base fee makes it expensive for zero-employee self-employed users
- Limited advanced reporting and customization
- No robust invoicing or time-tracking for solopreneurs
Best For
Self-employed individuals or micro-business owners who occasionally pay contractors and need simple 1099 compliance.
Pricing
Starts at $20/month + $5 per employee or contractor per payroll run; no free tier.
Conclusion
The top self-employed payroll software caters to diverse needs, with Gusto leading as the overall best, offering full-service payroll, HR, benefits, and automated tax filing. OnPay follows closely, standing out for affordability and unlimited runs, while QuickBooks Payroll impresses with its seamless integration with accounting software for self-employed professionals. Each tool excels in key areas, ensuring there’s an ideal fit for different business requirements.
Maximize your payroll efficiency by starting with Gusto, its end-to-end features simplify taxes, payments, and HR. For those prioritizing cost or accounting ties, OnPay and QuickBooks Payroll are strong alternatives—explore which aligns with your needs to streamline your operations.
Tools Reviewed
All tools were independently evaluated for this comparison
Referenced in the comparison table and product reviews above.