Quick Overview
- 1#1: Gusto - Automates payroll for employees and contractors including 1099 form generation, e-filing, and IRS compliance.
- 2#2: QuickBooks Online - Tracks contractor expenses and payments with seamless 1099 preparation and e-filing integration.
- 3#3: Rippling - Manages global contractor payroll, payments, and automated 1099 filings within a unified HR platform.
- 4#4: OnPay - Provides affordable unlimited payroll runs with built-in 1099 tracking and electronic filing.
- 5#5: ADP Run - Enterprise-grade payroll solution that handles contractor payments and 1099 form submissions.
- 6#6: Paychex - Full-service payroll platform supporting 1099 contractor management and IRS e-filing.
- 7#7: Patriot Software - Simple payroll software that generates, prints, and e-files 1099 forms for contractors.
- 8#8: Justworks - PEO platform that simplifies contractor payments and ensures 1099 compliance.
- 9#9: Track1099 - Specialized tool for importing data, creating, and e-filing 1099 forms directly with the IRS.
- 10#10: Tax1099 - Cloud-based service for preparing, mailing, and electronically filing 1099 information returns.
Tools were selected and ranked based on 1099-specific features (including e-filing and IRS integration), user experience, reliability, and overall cost to provide a comprehensive list of practical, high-quality solutions for diverse organizational needs.
Comparison Table
Navigating 1099 payroll in 2026 calls for dependable software, with leaders like Gusto, QuickBooks Online, Rippling, and OnPay delivering tailored options. This comparison table spotlights core features, user-friendliness, and pricing to pinpoint the ideal match for your contractor workflows.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Gusto Automates payroll for employees and contractors including 1099 form generation, e-filing, and IRS compliance. | enterprise | 9.7/10 | 9.8/10 | 9.5/10 | 9.2/10 |
| 2 | QuickBooks Online Tracks contractor expenses and payments with seamless 1099 preparation and e-filing integration. | enterprise | 8.7/10 | 9.2/10 | 8.4/10 | 7.9/10 |
| 3 | Rippling Manages global contractor payroll, payments, and automated 1099 filings within a unified HR platform. | enterprise | 8.8/10 | 9.2/10 | 8.5/10 | 8.0/10 |
| 4 | OnPay Provides affordable unlimited payroll runs with built-in 1099 tracking and electronic filing. | enterprise | 8.7/10 | 8.5/10 | 9.2/10 | 9.0/10 |
| 5 | ADP Run Enterprise-grade payroll solution that handles contractor payments and 1099 form submissions. | enterprise | 8.4/10 | 8.9/10 | 7.8/10 | 7.6/10 |
| 6 | Paychex Full-service payroll platform supporting 1099 contractor management and IRS e-filing. | enterprise | 7.8/10 | 8.5/10 | 7.5/10 | 7.0/10 |
| 7 | Patriot Software Simple payroll software that generates, prints, and e-files 1099 forms for contractors. | enterprise | 8.1/10 | 7.8/10 | 8.5/10 | 9.0/10 |
| 8 | Justworks PEO platform that simplifies contractor payments and ensures 1099 compliance. | enterprise | 7.8/10 | 8.2/10 | 8.5/10 | 7.0/10 |
| 9 | Track1099 Specialized tool for importing data, creating, and e-filing 1099 forms directly with the IRS. | specialized | 8.4/10 | 8.1/10 | 9.3/10 | 9.6/10 |
| 10 | Tax1099 Cloud-based service for preparing, mailing, and electronically filing 1099 information returns. | specialized | 7.4/10 | 7.7/10 | 8.1/10 | 6.9/10 |
Automates payroll for employees and contractors including 1099 form generation, e-filing, and IRS compliance.
Tracks contractor expenses and payments with seamless 1099 preparation and e-filing integration.
Manages global contractor payroll, payments, and automated 1099 filings within a unified HR platform.
Provides affordable unlimited payroll runs with built-in 1099 tracking and electronic filing.
Enterprise-grade payroll solution that handles contractor payments and 1099 form submissions.
Full-service payroll platform supporting 1099 contractor management and IRS e-filing.
Simple payroll software that generates, prints, and e-files 1099 forms for contractors.
PEO platform that simplifies contractor payments and ensures 1099 compliance.
Specialized tool for importing data, creating, and e-filing 1099 forms directly with the IRS.
Cloud-based service for preparing, mailing, and electronically filing 1099 information returns.
Gusto
enterpriseAutomates payroll for employees and contractors including 1099 form generation, e-filing, and IRS compliance.
End-to-end 1099 compliance with automatic form generation, threshold tracking, and direct e-filing to IRS and states
Gusto is a full-service payroll and HR platform that seamlessly handles 1099 contractor payments, including tracking, direct deposit or check issuance, and automated generation and e-filing of 1099-NEC and 1099-MISC forms with the IRS and states. It simplifies compliance by withholding forms until thresholds are met and integrates with accounting tools like QuickBooks and Xero for effortless reconciliation. Beyond basics, it offers contractor onboarding, time tracking, and expense reimbursements, making it a comprehensive solution for businesses managing independent contractors.
Pros
- Automated 1099 e-filing with IRS and multi-state support
- Seamless integrations with accounting software and easy contractor onboarding
- Direct deposit, checks, and payment approvals in one intuitive dashboard
Cons
- Pricing scales per contractor, which can add up for high-volume users
- Full platform features may feel excessive for 1099-only needs
- Requires base monthly fee even for low contractor counts
Best For
Small to mid-sized businesses managing 1099 contractors alongside W-2 employees who prioritize compliance and integrations.
Pricing
Contractor-only: $35/month base + $6/active contractor/month; full payroll plans start at $40/month + $6/person/month (billed annually).
QuickBooks Online
enterpriseTracks contractor expenses and payments with seamless 1099 preparation and e-filing integration.
Deep integration with QuickBooks accounting for automatic payment tracking and 1099 form population directly from your books
QuickBooks Online is a leading cloud-based accounting platform with integrated payroll capabilities that excel in managing 1099 independent contractors. It automatically tracks vendor payments, categorizes expenses, generates accurate 1099-NEC and 1099-MISC forms, and supports direct e-filing with the IRS and state agencies. This makes it a powerful all-in-one solution for businesses handling both accounting and contractor payroll compliance.
Pros
- Seamless integration with full accounting for automatic expense tracking and 1099 categorization
- Automated 1099 form generation, e-filing, and mailing services
- Unlimited contractor payments in higher plans with robust tax compliance tools
Cons
- Relatively high pricing, especially for businesses needing only 1099 features
- Requires a QuickBooks Online subscription, adding to overall cost
- Steeper learning curve for users new to the platform
Best For
Small to medium-sized businesses already using QuickBooks Online that need integrated accounting and reliable 1099 contractor management.
Pricing
Payroll Core starts at $50/month + $6 per employee/contractor; Premium $80/month + $6; Elite $125/month + $6 (1099 e-filing included in all plans; QuickBooks Online subscription required, starting at $30/month).
Rippling
enterpriseManages global contractor payroll, payments, and automated 1099 filings within a unified HR platform.
Unified global contractor payments and 1099 compliance integrated directly into the employee payroll workflow
Rippling is a comprehensive HR, payroll, and IT platform that provides robust 1099 payroll capabilities, including automated contractor payments, expense tracking, and IRS e-filing of 1099-NEC and 1099-MISC forms. It seamlessly integrates contractor management with employee payroll, onboarding, and compliance workflows. This makes it a powerful solution for businesses handling mixed W-2 and 1099 workforces, with global payment options for contractors.
Pros
- Automated 1099 form generation and IRS e-filing with high accuracy
- Seamless integration of contractor payments with employee payroll and HR tools
- Advanced contractor onboarding, approvals, and compliance automation
Cons
- Higher pricing makes it less ideal for small businesses needing only 1099 features
- Full platform can have a learning curve for users not utilizing HR/IT modules
- Custom quotes required, lacking transparent standalone 1099 pricing
Best For
Mid-sized to enterprise businesses managing both employees and contractors within a unified HR and payroll system.
Pricing
Custom enterprise pricing starting at $8 per active user/month (employees or contractors) plus $5-$10 per contractor payment and payroll processing fees; volume discounts available.
OnPay
enterpriseProvides affordable unlimited payroll runs with built-in 1099 tracking and electronic filing.
Guaranteed accurate 1099 e-filing to IRS and states with unlimited corrections at no extra cost
OnPay is a full-service payroll platform tailored for small businesses, offering robust support for both W-2 employees and 1099 independent contractors. It automates payroll calculations, tax withholdings, and seamless 1099-MISC and 1099-NEC form generation with e-filing to the IRS and states. The software integrates with accounting tools like QuickBooks, making it easy to track contractor payments and expenses alongside employee payroll.
Pros
- Unlimited payroll runs at a flat monthly rate plus per-person fee
- Expert support team handles 1099 filings and corrections with accuracy guarantee
- Strong integrations with QuickBooks, Xero, and Gusto for streamlined contractor management
Cons
- No built-in time tracking (requires integrations)
- Pricing scales with total active workers, which can add up for large contractor bases
- Limited advanced reporting customization for complex 1099 scenarios
Best For
Small to mid-sized businesses managing a mix of W-2 employees and 1099 contractors who need reliable, hassle-free 1099 e-filing without dedicated HR staff.
Pricing
$40 base monthly fee + $6 per active employee or contractor; free 1099 e-filing and unlimited runs included.
ADP Run
enterpriseEnterprise-grade payroll solution that handles contractor payments and 1099 form submissions.
Penalty-free tax filing guarantee, ensuring on-time and accurate 1099 submissions backed by ADP's expertise.
ADP Run is a cloud-based payroll platform from ADP tailored for small to mid-sized businesses, offering comprehensive processing for both W-2 employees and 1099 independent contractors. It automates 1099-MISC and 1099-NEC form generation, e-filing with the IRS, and state reporting, while integrating with full payroll features like direct deposit and tax calculations. The solution emphasizes compliance and scalability, making it suitable for growing teams with mixed workforce types.
Pros
- Robust 1099 e-filing and IRS compliance with accuracy guarantees
- Seamless integration for businesses handling both W-2 and 1099 payments
- Dedicated support and expert tax guidance
Cons
- Higher pricing that may not suit 1099-only users
- Steeper learning curve for non-payroll experts
- Additional fees for 1099 processing on top of base payroll costs
Best For
Small to mid-sized businesses with a mix of employees and contractors needing reliable, compliant 1099 handling alongside full payroll.
Pricing
Starts at around $59 base/month + $4-6 per employee/contractor per pay period; 1099 e-filing fees start at $5.50/form.
Paychex
enterpriseFull-service payroll platform supporting 1099 contractor management and IRS e-filing.
Integrated contractor payments via payroll runs with automatic 1099 form generation and e-filing
Paychex is a full-service payroll and HR platform that supports 1099 independent contractor management alongside W-2 employees, automating payments, tax calculations, and form generation. It handles 1099-NEC and 1099-MISC preparation, e-filing with the IRS and states, and mailing to recipients. While powerful for integrated payroll, it's less specialized as a standalone 1099 tool, making it suitable for growing businesses with mixed workforces.
Pros
- Seamless integration of 1099 filing with full payroll processing
- IRS-approved e-filing and multi-state compliance
- Dedicated support team and accuracy guarantees
Cons
- Higher pricing better suited for businesses with W-2 employees too
- Overkill and complex for 1099-only needs
- Custom quotes required, lacking transparent standalone 1099 plans
Best For
Mid-sized businesses managing both employees and contractors who want an all-in-one payroll solution with reliable 1099 compliance.
Pricing
Custom quotes starting at $59/month base for payroll + $5-$10 per 1099 form or employee/contractor; volume discounts available.
Patriot Software
enterpriseSimple payroll software that generates, prints, and e-files 1099 forms for contractors.
Guaranteed on-time 1099 e-filing with accuracy assurance and free corrections if errors occur.
Patriot Software offers affordable payroll solutions tailored for small businesses, with robust support for 1099 filing including e-filing of 1099-NEC and 1099-MISC forms directly to the IRS and states. Users can choose between in-house payroll processing with automated tax calculations or full-service options where Patriot handles everything. The platform emphasizes compliance, unlimited payroll runs, and direct deposit capabilities alongside 1099 management.
Pros
- Affordable pricing with no hidden fees for unlimited payrolls
- Seamless 1099 e-filing with IRS and state guarantees
- Responsive U.S.-based customer support
Cons
- Limited integrations with accounting software like QuickBooks
- Basic reporting and analytics compared to enterprise tools
- No standalone mobile app for on-the-go processing
Best For
Small businesses and freelancers managing a handful of 1099 contractors who prioritize cost-effective compliance over advanced features.
Pricing
Basic in-house payroll starts at $17 base + $4 per employee/month; full-service at $37 + $4/employee/month; 1099 filing included or $15 + $3.50/form standalone.
Justworks
enterprisePEO platform that simplifies contractor payments and ensures 1099 compliance.
Integrated payroll for both W2 and 1099 workers with automatic IRS e-filing and year-round corrections
Justworks is a full-service payroll and HR platform that supports 1099 independent contractors through automated payments, tax calculations, and 1099-MISC/NEC form generation with e-filing to the IRS. It integrates contractor management seamlessly with W2 employee payroll, offering compliance tools like state tax handling and payment tracking. While versatile for mixed workforces, it's not a standalone 1099 tool, making it suitable for businesses scaling beyond just contractors.
Pros
- Automated 1099 form preparation and e-filing with corrections support
- Seamless integration for paying contractors alongside W2 employees
- Strong compliance tools including multi-state tax handling
Cons
- Higher pricing model better suited for employee-heavy teams than contractor-only
- Requires base monthly fee even for low-volume 1099 users
- Less specialized 1099 features compared to dedicated tools like Track1099
Best For
Small to mid-sized businesses with a mix of W2 employees and 1099 contractors seeking an all-in-one payroll solution.
Pricing
Justworks Payroll: $40/month base + $6 per active person (employee or contractor); 1099 e-filing included at no extra cost.
Track1099
specializedSpecialized tool for importing data, creating, and e-filing 1099 forms directly with the IRS.
Unlimited free TIN matching to prevent IRS penalties during filing
Track1099 is a specialized cloud-based platform designed for small to medium businesses to easily create, file, and manage 1099 forms like 1099-NEC and 1099-MISC. It supports bulk uploads from Excel or CSV, TIN matching to avoid penalties, and direct e-filing with the IRS and multiple states. The software focuses on compliance and simplicity rather than full payroll processing, making it ideal for handling independent contractor tax forms without complexity.
Pros
- Extremely affordable pay-per-form pricing
- Simple bulk import from spreadsheets
- Reliable e-filing with TIN matching included
Cons
- No integration with payroll disbursement systems
- Limited advanced reporting and analytics
- Basic recipient management without automation
Best For
Small businesses and accountants who need straightforward, low-cost 1099 form filing without full payroll features.
Pricing
Free for up to 5 forms; pay-per-form at $2.90 each or annual subscriptions starting at $49 for 25 forms.
Tax1099
specializedCloud-based service for preparing, mailing, and electronically filing 1099 information returns.
Bulk Excel/CSV upload with automated TIN matching and real-time IRS e-filing status
Tax1099 is a web-based platform designed for preparing and e-filing 1099 forms, including 1099-NEC and 1099-MISC, directly with the IRS and state agencies. It supports bulk uploads from Excel or CSV files, TIN matching to prevent penalties, and handling corrections or amendments. While focused on tax form compliance rather than full payroll processing, it streamlines year-end reporting for businesses with independent contractors.
Pros
- Simple bulk import from spreadsheets for high-volume filers
- IRS-approved e-filing with TIN matching and state support
- Affordable for low-volume users with free corrections
Cons
- Lacks comprehensive payroll features like payment tracking or invoicing
- Pay-per-form pricing escalates with volume without flat-rate options
- Limited integrations with major accounting software
Best For
Small businesses or accountants needing quick, compliant 1099 e-filing without advanced payroll management.
Pricing
Pay-per-form: $3.49 for up to 10 forms, $2.49 for 11-100, $1.49 for 101+; volume bundles and free corrections available.
Conclusion
The top 10 tools span from full-service enterprise solutions to specialized 1099-focused platforms, each designed to simplify payroll and compliance. Gusto leads as the top choice, excelling in automation for 1099 form generation, e-filing, and IRS adherence. QuickBooks Online and Rippling follow closely, with standouts in integration tools and global management, respectively, ensuring there’s a strong option for nearly every business need.
Don’t let 1099 management become a hassle—grab Gusto to handle filings and compliance smoothly, or dive into the alternatives to find the tool that aligns best with your workflow.
Tools Reviewed
All tools were independently evaluated for this comparison