Quick Overview
- 1#1: Gusto - Gusto automates payroll processing, 1099 filings, and payments for independent contractors with seamless compliance for small businesses.
- 2#2: OnPay - OnPay delivers affordable, full-service payroll including unlimited 1099 contractor payments and automated tax filings.
- 3#3: QuickBooks Payroll - QuickBooks Payroll integrates contractor payments, 1099 e-filing, and accounting for freelancers and small teams.
- 4#4: Rippling - Rippling unifies HR, IT, and payroll to manage global independent contractors with automated compliance and payments.
- 5#5: Deel - Deel handles international contractor payroll, contracts, and compliance in 150+ countries with localized payments.
- 6#6: ADP - ADP provides scalable payroll solutions for 1099 contractors with robust reporting, tax filing, and integrations.
- 7#7: Paychex - Paychex offers contractor payroll management with automated 1099 forms, direct deposits, and HR support.
- 8#8: Remote - Remote simplifies hiring and paying global independent contractors with compliant payroll and EOR services.
- 9#9: Justworks - Justworks manages contractor and employee payroll through a PEO model with 1099 support and benefits access.
- 10#10: Papaya Global - Papaya Global streamlines multi-country contractor payroll with real-time compliance and payment automation.
These tools were selected based on robust feature sets (automated tax filings, multi-country support, seamless integrations), user experience, and overall value, ensuring they deliver reliable performance across varying business requirements.
Comparison Table
Discover how to streamline independent contractor payroll with this comparison table, which analyzes top tools like Gusto, OnPay, QuickBooks Payroll, Rippling, and Deel. Learn key features, pricing structures, and capabilities to find the best fit for your business needs.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Gusto Gusto automates payroll processing, 1099 filings, and payments for independent contractors with seamless compliance for small businesses. | specialized | 9.4/10 | 9.6/10 | 9.3/10 | 8.9/10 |
| 2 | OnPay OnPay delivers affordable, full-service payroll including unlimited 1099 contractor payments and automated tax filings. | specialized | 9.2/10 | 9.0/10 | 9.5/10 | 9.4/10 |
| 3 | QuickBooks Payroll QuickBooks Payroll integrates contractor payments, 1099 e-filing, and accounting for freelancers and small teams. | specialized | 8.7/10 | 9.2/10 | 8.5/10 | 8.0/10 |
| 4 | Rippling Rippling unifies HR, IT, and payroll to manage global independent contractors with automated compliance and payments. | enterprise | 8.6/10 | 9.2/10 | 8.4/10 | 8.0/10 |
| 5 | Deel Deel handles international contractor payroll, contracts, and compliance in 150+ countries with localized payments. | specialized | 8.6/10 | 9.1/10 | 8.4/10 | 8.0/10 |
| 6 | ADP ADP provides scalable payroll solutions for 1099 contractors with robust reporting, tax filing, and integrations. | enterprise | 8.2/10 | 8.7/10 | 7.4/10 | 7.6/10 |
| 7 | Paychex Paychex offers contractor payroll management with automated 1099 forms, direct deposits, and HR support. | enterprise | 7.8/10 | 8.2/10 | 7.4/10 | 7.1/10 |
| 8 | Remote Remote simplifies hiring and paying global independent contractors with compliant payroll and EOR services. | specialized | 8.1/10 | 8.5/10 | 7.9/10 | 7.6/10 |
| 9 | Justworks Justworks manages contractor and employee payroll through a PEO model with 1099 support and benefits access. | enterprise | 7.9/10 | 8.2/10 | 8.5/10 | 7.0/10 |
| 10 | Papaya Global Papaya Global streamlines multi-country contractor payroll with real-time compliance and payment automation. | enterprise | 8.1/10 | 9.2/10 | 7.4/10 | 7.0/10 |
Gusto automates payroll processing, 1099 filings, and payments for independent contractors with seamless compliance for small businesses.
OnPay delivers affordable, full-service payroll including unlimited 1099 contractor payments and automated tax filings.
QuickBooks Payroll integrates contractor payments, 1099 e-filing, and accounting for freelancers and small teams.
Rippling unifies HR, IT, and payroll to manage global independent contractors with automated compliance and payments.
Deel handles international contractor payroll, contracts, and compliance in 150+ countries with localized payments.
ADP provides scalable payroll solutions for 1099 contractors with robust reporting, tax filing, and integrations.
Paychex offers contractor payroll management with automated 1099 forms, direct deposits, and HR support.
Remote simplifies hiring and paying global independent contractors with compliant payroll and EOR services.
Justworks manages contractor and employee payroll through a PEO model with 1099 support and benefits access.
Papaya Global streamlines multi-country contractor payroll with real-time compliance and payment automation.
Gusto
specializedGusto automates payroll processing, 1099 filings, and payments for independent contractors with seamless compliance for small businesses.
End-to-end 1099 compliance with automatic IRS e-filing and contractor delivery
Gusto is a leading payroll platform that simplifies independent contractor management by enabling seamless ACH payments, expense tracking, and automated 1099-NEC form generation and IRS e-filing. It offers a dedicated Contractors plan tailored for businesses handling 1099 workers without needing full employee payroll features. With strong compliance tools and integrations with accounting software like QuickBooks, Gusto ensures accurate tax reporting and payment history organization for contractors.
Pros
- Automated 1099 filing and distribution directly to contractors and IRS
- Quick ACH payments with built-in invoicing and expense reimbursement
- Robust integrations with popular accounting tools and time-tracking apps
Cons
- Pricing scales per active contractor, which can add up for high volumes
- Primarily US-focused, lacking international contractor support
- Overkill for very small teams needing only basic payments
Best For
Small to medium businesses managing multiple independent contractors who require compliant 1099 handling and integrated payroll.
Pricing
Contractors plan starts at $35/month base + $6 per active contractor/month; no long-term contracts required.
OnPay
specializedOnPay delivers affordable, full-service payroll including unlimited 1099 contractor payments and automated tax filings.
Unlimited 1099 e-filing and preparation at no extra cost
OnPay is a full-service payroll platform tailored for small businesses, excelling in handling independent contractor payments alongside employee payroll with features like direct deposit, payment tracking, and automated 1099 preparation. It offers unlimited 1099 contractors, e-filing of forms, and compliance tools to simplify tax withholding and reporting. The software integrates seamlessly with accounting tools like QuickBooks and provides expert support for multi-state contractor payments.
Pros
- Affordable all-in-one pricing with taxes and 1099 filings included
- Intuitive interface with quick setup for contractor payments
- Strong integrations and dedicated US-based support
Cons
- Full payroll platform may feel overkill for contractors-only users
- No support for international contractors
- Limited advanced contractor-specific reporting
Best For
Small businesses paying multiple US-based independent contractors alongside a modest employee roster.
Pricing
$40 base fee per month + $6 per person paid (employees or contractors), taxes and filings included; free for first month.
QuickBooks Payroll
specializedQuickBooks Payroll integrates contractor payments, 1099 e-filing, and accounting for freelancers and small teams.
Deep integration with QuickBooks Online that automatically categorizes contractor payments as expenses and generates invoices
QuickBooks Payroll, offered by Intuit, is a robust payroll platform integrated with QuickBooks accounting software, enabling businesses to manage payments, taxes, and compliance for independent contractors alongside W-2 employees. It automates 1099-MISC and 1099-NEC form generation, e-filing with the IRS, and direct payments via ACH or direct deposit. The tool tracks contractor expenses, invoices, and payments within the QuickBooks ecosystem, streamlining financial workflows for small businesses.
Pros
- Seamless integration with QuickBooks Online for unified accounting and payroll tracking
- Automated 1099 form creation, e-filing, and IRS compliance
- Direct contractor payments with next-day direct deposit options
Cons
- Higher pricing compared to contractor-only specialized tools
- Overkill for businesses solely using independent contractors without employees
- Full features require QuickBooks Online subscription and higher-tier plans
Best For
Small to medium businesses already using QuickBooks that manage a mix of W-2 employees and independent contractors.
Pricing
Starts at $45/month + $6 per employee/contractor (Core plan); contractor payments available without employee add-ons, with annual 1099 e-filing included.
Rippling
enterpriseRippling unifies HR, IT, and payroll to manage global independent contractors with automated compliance and payments.
Global contractor payments in 120+ countries with automatic tax withholding and compliance built-in
Rippling is an all-in-one workforce management platform that streamlines HR, IT, payroll, and finance for businesses. For independent contractor payroll, it provides automated 1099 form generation and e-filing, global payments in 120+ countries, and contract management integrated with employee systems. This makes it ideal for scaling companies handling mixed workforces, ensuring compliance and efficiency without multiple tools.
Pros
- Automated 1099-MISC/NEC filing and IRS e-submission
- Global contractor payments with multi-currency support and low fees
- Seamless integration with employee payroll and HR tools
Cons
- Higher cost for small businesses focused solely on contractors
- Full feature set can feel overwhelming for simple payroll needs
- Pricing scales with employee headcount even for contractor-heavy use
Best For
Mid-sized businesses managing both employees and international contractors who want a unified platform for payroll and compliance.
Pricing
Core platform starts at $8/user/month; contractor payments are pay-as-you-go with fees from 0.5% + $0.25 per transaction, plus payroll add-ons.
Deel
specializedDeel handles international contractor payroll, contracts, and compliance in 150+ countries with localized payments.
Seamless global compliance automation that generates localized contracts and handles tax forms without needing local entities.
Deel is a global workforce management platform specializing in independent contractor payroll, compliance, and payments across 150+ countries. It automates onboarding with customizable contracts, handles multi-currency payouts via bank transfers, PayPal, and crypto, and ensures local tax compliance without requiring employer-of-record services. Businesses can track invoices, timesheets, and expenses in a unified dashboard, making it suitable for scaling remote teams internationally.
Pros
- Extensive global coverage with payments in 120+ currencies and compliance in 150+ countries
- Automated contract generation and invoicing streamline contractor management
- Integrations with tools like QuickBooks, Xero, and Slack enhance workflow efficiency
Cons
- Pricing scales per active contractor, which can be costly for small or low-volume teams
- Advanced compliance features have a learning curve for non-HR users
- Payment processing times vary by country, occasionally exceeding 5 business days
Best For
Mid-sized companies and enterprises hiring international independent contractors who need compliant, multi-currency payroll without local subsidiaries.
Pricing
Starts at $49 per active contractor/month for management (Deel Pro plan); pay-as-you-go options with transaction fees of 0.5-2% per payment.
ADP
enterpriseADP provides scalable payroll solutions for 1099 contractors with robust reporting, tax filing, and integrations.
Automated 1099 e-filing and distribution integrated with full payroll ecosystem
ADP provides robust payroll solutions tailored for businesses managing independent contractors, including automated payments, invoicing, expense tracking, and 1099-MISC/1099-NEC form generation and e-filing. It integrates contractor management seamlessly with full employee payroll and HR tools via platforms like ADP RUN and Workforce Now. This makes it ideal for scaling operations while ensuring compliance with federal, state, and local tax regulations for non-employee compensation.
Pros
- Comprehensive 1099 compliance and automated tax filings
- Scalable integration with employee payroll and HR systems
- Reliable customer support from a established provider
Cons
- Higher pricing that may not suit small-scale users
- Steeper learning curve for non-HR experts
- Overkill for businesses focused solely on contractors
Best For
Mid-sized businesses with mixed employee and contractor workforces seeking enterprise-grade compliance and scalability.
Pricing
Custom quotes starting at around $20-$50 per contractor/month plus base platform fees ($100+/month); scales with volume.
Paychex
enterprisePaychex offers contractor payroll management with automated 1099 forms, direct deposits, and HR support.
Guaranteed IRS-compliant 1099 e-filing with expert review and corrections if needed
Paychex is a comprehensive payroll and HR platform that supports independent contractor management through features like 1099 form generation, e-filing, and direct payments. It integrates contractor payments seamlessly with full employee payroll processing, ensuring compliance with tax regulations. Ideal for businesses scaling from contractors to full teams, it offers robust reporting and automation to streamline contractor payouts and year-end filings.
Pros
- Automated 1099 e-filing and IRS compliance guarantees
- Seamless integration with employee payroll for hybrid workforces
- Dedicated customer support and expert tax guidance
Cons
- Higher pricing better suited for businesses with employees, not contractor-only
- Steeper learning curve for users new to full payroll systems
- Less flexibility for one-off or low-volume contractors
Best For
Small to mid-sized businesses managing both W-2 employees and 1099 contractors who need reliable compliance and scalability.
Pricing
Custom quotes starting around $80/month base + $5-$6 per participant (employee or contractor), with add-ons for advanced features.
Remote
specializedRemote simplifies hiring and paying global independent contractors with compliant payroll and EOR services.
Automated global compliance engine that handles local tax, labor laws, and payment regulations in 170+ countries
Remote (remote.com) is a global workforce management platform with robust independent contractor payroll features, enabling businesses to hire, onboard, pay, and manage contractors in over 170 countries. It automates invoicing, multi-currency payments, compliance checks, and contract generation, reducing administrative burdens for distributed teams. Ideal for scaling companies, it integrates payroll with HR tools for seamless operations across borders.
Pros
- Extensive global coverage in 170+ countries with automated compliance
- Seamless multi-currency payments and invoicing
- Integrated contract templates and onboarding tools
Cons
- Premium pricing may not suit small teams or low-volume users
- Limited advanced payroll customization options
- Customer support response times can vary
Best For
Mid-sized companies managing international independent contractors who need compliant global payroll without local entities.
Pricing
Contractor Management starts at $29 per active contractor per month, plus payment fees (e.g., 1-2% for bank transfers).
Justworks
enterpriseJustworks manages contractor and employee payroll through a PEO model with 1099 support and benefits access.
Integrated employee and contractor payroll with co-employment benefits access
Justworks is a comprehensive payroll and HR platform that supports independent contractor management, including automated payments, 1099 filings, and compliance tools. It integrates contractor payroll with employee payroll in a single dashboard, making it suitable for mixed workforces. The software automates invoicing, expense reimbursements, and tax calculations while providing worker classification guidance to minimize risks.
Pros
- Unified payroll for employees and contractors
- Automated 1099-NEC filings and payments
- Robust compliance and misclassification support
Cons
- Higher pricing better suited for larger teams
- Less optimized for contractor-only businesses
- Custom quotes can obscure transparent costs
Best For
Small to mid-sized businesses with a mix of W2 employees and 1099 contractors needing integrated HR and payroll.
Pricing
Quote-based; typically $59 per active contractor/employee per month plus a $99+ base fee.
Papaya Global
enterprisePapaya Global streamlines multi-country contractor payroll with real-time compliance and payment automation.
One-click global contractor payments with automated local tax compliance and withholding in 160+ countries
Papaya Global is a global workforce management platform specializing in payroll, payments, and compliance for independent contractors across 160+ countries. It automates multi-currency payments, tax withholding, and regulatory compliance, while integrating with HRIS systems for streamlined contractor management. The platform provides real-time dashboards for tracking payments and expenses, making it suitable for distributed teams.
Pros
- Extensive global coverage in 160+ countries with local compliance
- Automated multi-currency payments and tax management
- Seamless integrations with major HRIS and accounting tools
Cons
- Enterprise-level pricing that's expensive for small businesses
- Steep learning curve and complex onboarding process
- Overkill for domestic-only contractor payroll needs
Best For
Mid-to-large enterprises managing international networks of independent contractors requiring robust global compliance and payments.
Pricing
Custom enterprise pricing starting at around $5,000/month based on workforce size; contact sales for tailored quotes.
Conclusion
After reviewing the 10 featured tools, Gusto clearly stands as the top choice, excelling in seamless automation for payroll processing, 1099 filings, and payments, with robust compliance tailored for small businesses. OnPay and QuickBooks Payroll follow as strong alternatives: OnPay offers affordable, full-service support with unlimited 1099 payments, while QuickBooks Payroll integrates contractor management with accounting needs. These options ensure flexibility, making it easier for businesses to find the right fit for their unique contractor payroll requirements.
Take the first step in simplifying your contractor payroll—try Gusto, the top-ranked solution, to streamline payments, filings, and compliance, and set your business up for smooth operations.
Tools Reviewed
All tools were independently evaluated for this comparison