When managing contractor payments, there is a high risk of compliance issues due to inconsistent 1099-NEC filing, fragmented payment tracking, and misclassified workers, which results in costly penalties for companies. Many generic payroll tools lack specialized workflows that are required for contractor teams.
To determine the best 1099 payroll solutions, we evaluated the platforms based on 1099 filing accuracy, payment flexibility, contractor onboarding efficiency, and compliance safeguards. In this guide, we have shortlisted the best payroll software for 1099 employees to help users find the right solution.
Software | Ratings | Trial Info | Starting Price | Best For | Key Features |
Gusto HR Software (Editor’s Choice) | 4.6/5
| NA
View Demo | $35/month ($6/contractor/month)
Get A Custom Quote | e-filing 1099 | Employee Benefits, HR Tools, Time Tracking
|
4.4/5
| 30-day free trial
View Demo | $25/month ($2/additional contractor) Get A Custom Quote | Send Unlimited 1099s | Same-Day Direct Deposit, Automatic Payroll, Time Tracking Management | |
4.8/5
| NA
View Demo | $49/month ($6/worker per month)
Get A Custom Quote | Unlimited Monthly Pay Runs | Org Charts, Employee Onboarding, Reporting And Analytics | |
4.7/5
| 6-month free trial
View Demo | Custom Pricing
Get A Custom Quote | Mobile Accessibility | HCM Managed Services, HR Outsourcing, Payroll Taxes | |
4.9/5
| NA
View Demo | $8/employee/month
Get A Custom Quote | Global Contractor Management | Rippling PEO, Permissions and Policies, Workflow Studio | |
4.8/5
|
View Demo | $49/contractor/month
Get A Custom Quote | Flexible Payout Options | Global People Platform, Self-Serve Onboarding, Document Management | |
4.5/5
| NA
View Demo | $8/employee/month + ($50/month base fee)
Get A Custom Quote | Global Payroll | Payroll Processing | |
4.5/5
| 6-months free trial
View Demo | $29/month + $7 per employee
Get A Custom Quote | Automatic Payroll Scheduling | Direct Deposits, Online Pay Stubs, 1099 Form Filing | |
4.7/5
| 30-day free trial
View Demo | $6/person/month
Get A Custom Quote | Automatic Payroll Tax Filing | Automated Tax Filings, Labor-Cost Reporting, Streamlined Onboarding | |
4.6/5
| 30-day free trial
View Demo | $17/month
Get A Custom Quote | Contractor Self-Service Portal | Payroll Management, Payroll Reporting, Tax Compliance |
Gusto is a full-service payroll software for both employees and contractors that streamlines the payment process for businesses working with 1099 contractors. It allows businesses to quickly add contractors, set up recurring or one-time payments, and send funds via direct deposit. Moreover, the software automatically generates and files 1099 forms, which reduces year-end administrative hassle and ensures it complies with the Internal Revenue Service (IRS) regulations.
Pros And Cons
Pros | Cons |
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Best For
Gusto is an ideal choice for companies that hire contractors and 1099 employees in the healthcare, retail, technology, and manufacturing sectors.
Key Features
- Employee Benefits
- HR Tools
- Time Tracking
- Compliance
- Reporting
Pricing
Gusto pricing starts at $35/month and $6/contractor/month for its Contractor Only plan. The vendor offers flexible, transparent pricing plans for individuals and organizations, which include:
- Simple - $49/month (plus $6/person/month)
- Plus - $80/month (plus $12/person/month)
- Premium - $180/month (plus $22/person/month)
- Solo - $49/month (plus $6/person/month)
Disclaimer: The pricing is subject to change.
Why We Like It
What sets Gusto apart is that it handles contractor payments in 120+ countries. The platform is suitable for businesses scaling contractor teams by supporting global payments in various currencies and ensuring international compliance. These capabilities place Gusto at the top of this list. We recommend it for businesses expanding internationally that need a reliable way to manage compliance, payments, and contractor data in one system.
User Ratings
User feedback highlights that Gusto is praised for its automatic tax filing features. However, some of the users encountered system glitches and problems during account signup.
QuickBooks is a cloud-based software that automates payments, tax filings, and compliance processes to pay 1099 employees. It helps organizations pay contractors through direct deposit and automatically generate 1099-NEC forms. Additionally, the software stores contractor information securely and syncs with accounting data, which ensures smooth bookkeeping and compliance.
Pros And Cons
Pros | Cons |
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Best For
It is an ideal choice for businesses in the legal, construction, manufacturing, and wholesale sectors that work with contractors and need to send unlimited 1099s.
Key Features
- Same-Day Direct Deposit
- Automatic Payroll
- Time Tracking Management
- Employee Benefits Administration
- Tax Filing And Compliance
Pricing
QuickBooks pricing starts at $25/month for its Contractor Payments plan, which includes 20 contractors, and $2 for each additional contractor. Other pricing plans include
- Contractor Payments and Simple Start - $63/month
- Payroll Core - $50/month
The vendor also offers four pricing plans for small and mid-sized businesses, which include:
- Simple Start - $38/month
- Essentials - $75/month
- Plus - $115/month
- Advanced - $275/month
Disclaimer: The pricing is subject to change.
Why We Like It
The software earns its place in the list of best payroll software for 1099 employees due to next-day direct deposit. It gives flexibility to businesses without compromising the payment speed. The software processes contractor payments faster than traditional check processing through direct deposit automation and integrated payroll workflows. This eliminates month-end reconciliation while maintaining an audit trail that flows directly into automated 1099 preparation.
User Ratings
According to numerous customer feedback, the software is appreciated for its integration with QuickBooks accounting. In contrast, some users faced issues with tax filing accuracy, including delays in resolving payroll tax notices and incorrect tax calculations.
OnPay Payroll offers full-service payroll, tax filing, benefits administration, and basic HR tools like onboarding and document storage. It helps businesses pay contractors through checks or direct deposits, keep accurate payment records, and automatically generate e-file 1099-NEC forms at the end of the year. Furthermore, its contractor support ensures businesses stay compliant with tax laws while minimizing manual admin work.
Pros And Cons
Pros | Cons |
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Best For
Businesses in the construction, education, healthcare, legal, and non-profit sectors are looking for flexible 1099 payroll software for unlimited monthly pay runs.
Key Features
- Org Charts
- Employee Onboarding
- Reporting And Analytics
- Self-Service Portal
- PTO Tracking
- Health Insurance
Pricing
OnPay Payroll pricing starts at $45/month with an additional $6/worker/month for its Payroll Essentials plan.
Disclaimer: The pricing is subject to change.
Why We Like It
We like OnPay Payroll for its payroll reports that pay contractors through direct deposits. Its built-in payroll reports help users get a clear view of contractor payments through the intuitive dashboard. Also, the platform generates and e-files 1099-NEC for year-end tax reporting. If you manage a distributed freelance team or rely on project-based contractors, OnPay keeps payments clean, documented, and audit-ready with minimal admin overhead.
User Ratings
Based on user reviews, OnPay Payroll is praised for its easy-to-use and straightforward setup process. However, a few of them noted that the platform offers limited third-party integrations.
RUN Powered By ADP is a payroll and HR solution for businesses that fully support paying, managing, and onboarding 1099 independent contractors. It enables automatic 1099 filing, secure digital contractor onboarding, direct deposit payments, and 24/7 access for contractors to retrieve their tax documents.
Pros And Cons
Pros | Cons |
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Best For
The software is best for organizations in the hospitality, retail, finance, and government sectors looking for a user-friendly mobile app for payroll processing.
Key Features
- Faster And Easier Payroll
- Flexibility And Compliance Built-in
- Expert Hiring And HR Support
- Integrate Add-Ons Seamlessly
- ADP RUN Payroll
- Workforce Management
- HCM Managed Services
- HR Outsourcing
- Payroll Taxes
Pricing
The vendor offers customized RUN Powered By ADP pricing plans, which include Essential Payroll, Enhanced Payroll, Complete Payroll And HR+, and HR Pro Payroll and HR. The pricing depends on the business size and specific requirements.
Disclaimer: The pricing is subject to change.
Why We Like It
We recommend users choose this software for its ADP WorkMarket integration, which allows contractors to select and access the preferred payment method. It generates invoices on behalf of contractors depending on the pre-set payment terms. For businesses that need to manage hundreds of contractors with urgent cash flow needs, this is a great choice. This improves contractor retention and satisfaction in tight labor markets.
User Ratings
Verified user reviews highlight that the platform's customer support team is responsive. On the flip side, some reviewers report login timeouts and glitches.
Rippling is a cloud-based workforce management platform that streamlines everything businesses need to hire, manage, grow, and pay employees. It offers a global payroll module that allows businesses to manage their entire workforce, including employees and 1099 contractors. Furthermore, the system processes unlimited contractor payments and handles multi-currency payments to contractors.
Pros And Cons
Pros | Cons |
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Best For
Organizations of all sizes in the construction, finance, retail, manufacturing, and healthcare sectors are looking for a platform offering global contractor management.
Key Features
- Benefits Administration
- Global Workforce Management
- Global Payroll
- Rippling PEO
- Rippling HR Services
- Permissions And Policies
- Workflow Studio
- Approval Management
- Reporting And Analytics
- App Studio
Pricing
Rippling pricing starts at $8/employee/month. The tool is divided into the following core modules with custom pricing:
- Rippling Platform - $35/month + $8/employee/month
- Rippling IT – Custom pricing
- Rippling Spend – Custom pricing
Disclaimer: Pricing references are based on publicly available third-party information and industry benchmarks. Actual costs may vary.
Why We Like It
If you work with an international or distributed contractor based, Rippling gives control over the contractor's payments, which includes how and when the funds move. It allows contractors to check their available funds and initiate withdrawals to their bank accounts on their own schedule. For international contractors facing currency volatility or regional banking delays, this self-service withdrawal model provides financial control.
User Ratings
Customer reviews highlight that the software offers workflow automation across the IT and HR processes. On the other hand, some users have encountered occasional system glitches that disrupt workflows.
Deel software is a cloud-based payroll software that helps companies with international hiring, paying, and employee and contractor management. It enables companies to onboard, pay, and manage staff across 200+ countries through an integrated all-in-one system. Furthermore, Deel automatically generates and e-files 1099-NEC forms for US contractors and provides contracts and classification assessments that adapt to regional labor laws.
Pros And Cons
Pros | Cons |
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Best For
Deel is well-suited for organizations of all sizes in the fintech, gaming, advertising, and crypto sectors that let contractors withdraw payments in flexible payout options.
Key Features
- Global People Platform
- Self-Serve Onboarding
- Document Management
- Learning And Development
- Performance Reviews
Pricing
Deel pricing starts at $49/contractor/month for its Standard plan. It also offers another pricing plan, Contractor Of Record, with a price starting at $325/contractor/month. Furthermore, the payroll pricing plans of the software include:
- Global - $29/employee/month
- US - $24/employee/month
- Self-Serve Payroll – Custom Pricing
Disclaimer: The pricing is subject to change.
Why We Like It
We suggest users choose this platform for its Deel Card, which allows contractors to hold and spend their USD earnings to address the currency instability challenge. Contractors get the virtual card that functions as a prepaid Mastercard, which enables them to spend directly from their Deel balance. For contractors working in different regions, this card provides financial stability by protecting their income from devaluation and maintaining global spending flexibility.
User Ratings
Based on user feedback, the software is appreciated for its user-friendly interface for managing payroll workflows. However, a few users complained about the customer support team regarding slow responses.
Justworks is a Professional Employer Organization (PEO) that combines payroll and HR compliance for organizations managing 1099 employees. It generates and e-files 1099-NEC and 1099-MISC forms and tracks annual payments for precise tax reporting.Organizations can add external payment amounts for comprehensive 1099 preparation. Moreover, its online portals are secure enough to help contractors access their tax documents alongside payment history.
Pros And Cons
Pros | Cons |
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Best For
The tool suits organizations in healthcare, finance, real estate, and manufacturing sectors looking for global payroll functionality to pay contractors on time.
Key Features
- Payroll Processing
- Benefits Administration
- HR Tools
- Compliance Support
- Time Tracking
Pricing
Justworks pricing starts at $8/employee/month and includes a $50/month base fee for its Payroll plan. Other pricing plans of the software include:
- PEO Basic - $79/employee/month
- PEO Plus - $109/employee/month
- EOR - $599/employee/month
Disclaimer: The pricing is subject to change.
Why We Like It
Justworks sets itself apart for its international contractor payments, that consolidates global and domestic contractor management into a single platform. This eliminates the need for separate payment processors or multiple logins. Businesses can pay contractors in 60+ countries in local currencies or USD. Also, it handles currency conversion at current exchange rates and provides self-service contractor onboarding.
User Ratings
User feedback reveals that customer support is responsive during the setup process. However, some users say that it lacks advanced HR features.
SurePayroll is a cloud-based payroll software that allows businesses to add and pay 1099 employees. It calculates wages and handles direct deposit or check payments and automatically prepares and files 1099-NEC forms. Furthermore, the tool handles federal, state, and local tax payments and filings for businesses that opt for the full-service plan.
Pros And Cons
Pros | Cons |
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Best For
The tool is best for 1099 employees in hospitality, legal firms, healthcare, and construction, looking for automatic payroll scheduling.
Key Features
- Direct Deposits
- Online Pay Stubs
- 1099 Form Filing
- Unlimited Payroll Runs
- New Hire Reporting
- Labor Law Posters
- Multiple Pay Rates
Pricing
SurePayroll pricing starts at $29/month + $7/employee. Also, it offers a No Tax Filing plan starting at $20/month + $4/employee.
Disclaimer: The pricing is subject to change.
Why We Like It
We suggest SurePayroll for its unified payment tracking system that gathers all the contractor's payment documentation, year-end tax preparation, and invoices into centralized records. It maintains detailed logs of the transactions related to the contractors and calculates the total annual payment. This eliminates the fragmented spreadsheets and folder approach that creates gaps in documentation. For organizations that manage variable project schedules with contractors, SurePayroll keeps records organized during IRS audits and tax season.
User Ratings
Most of the user reviews highlight that the tool is praised for its user-friendly payroll processing. However, a few reviewers noted mistakes in tax filings.
9. Square Payroll
Square Payroll is a powerful software solution to help businesses manage payroll processing for contractors. It offers automated tax filings and payments, ensuring compliance with federal and state regulations. With everything accessible from Square’s dashboard, businesses using Square for sales can keep contractor payments in the same system they use for day-to-day operations.
Pros And Cons
Pros | Cons |
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Best For
Suitable for retail, food, home maintenance, and contractors, the tool automates the process of calculating payroll tax and filings.
Key Features
- Automated Tax Filings
- Labor-Cost Reporting
- Streamlined Onboarding
- Instant Deposit
- Benefits Administration
Pricing
Square Payroll pricing starts at $6/person/month for its Contractor Only Payroll plan. Also, it offers a Full-Service Payroll plan, starting at $35/month + $6/employee/month.
Disclaimer: The pricing is subject to change.
Why We Like It
Square Payroll is the best choice for businesses that are looking for a smooth integration between the contractor and payroll payments. It easily runs payroll in minutes, automatically sends payments to contractors, and issues 1099-NEC forms. This integration cuts down admin work and keeps contractor payouts consistent with the rest of the finances within an organization.
User Ratings
User feedback appreciates the software for its transparent pricing and responsive customer support. In contrast, some reviewers mentioned that the software offers limited features compared to large payroll solutions.
10. Patriot Payroll
Patriot Payroll is a small-business payroll platform that handles payments for both W-2 employees and 1099 contractors in one system. It lets businesses set up contractors, process unlimited payroll runs with direct deposit or printed checks, and optionally e-file 1099 forms. Moreover, the platform brings employee and contractor payments into a single, easy-to-manage system.
Pros And Cons
Pros | Cons |
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Best For
The software is designed for businesses across retail, healthcare, and real estate, looking for a platform that offers a contractor self-service portal to view 1099 tax forms.
Key Features
- Payroll Management
- Payroll Reporting
- Tax Compliance
- W-2 Preparation
- Compensation Management
Pricing
Patriot Payroll Pricing starts at $17/month + $4/employee or contractor/month as the base price. Also, the software offers a Full-Service Payroll plan with a price starting at $37/month + $5/employee or contractor/month.
Disclaimer: The pricing is subject to change.
Why We Like It
What makes Patriot stand out for 1099 contractor payroll is its connection to bookkeeping support that keeps contractor pay aligned with the financial records. It categorizes contractor expenses and reconciles accounts, which helps see the impact of contractor payments on the books. If you run a small business where payroll and basic finance overlap, this setup reduces errors and saves time.
User Ratings
According to user reviews, the Patriot Payroll stands out for its automated tax filing and calculations. However, some users faced challenges in multi-pay scenarios.
11. Tax1099.com
Tax1099.com is an IRS-authorized e-filing platform specializing in 1099 form preparation and filing for businesses managing contractor workforces. It handles 1099-NEC, 1099-K, and 1099-MISC forms. Moreover, Tax1099.com simplifies filing and compliance by generating 1099 forms from payment data, e-filing them with the IRS, and delivering copies to contractors for handling independent payments.
Pros And Cons
Pros | Cons |
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Best For
The software is ideal for small, medium, and large-sized businesses, and accounting firms, seeking a platform that corrects form content even after acceptance from the IRS.
Key Features
- AI Smart eFiling
- IRS-Compliant eDelivery
- Pre-Built Reports
- Bulk TIN Matching
- Audit Trails
- Two Factor Authentication
- PII Data Security
Pricing
Tax1099.com pricing starts at $249/year for its Team plan. Further pricing plans include:
- Essential – Free
- Scale - $249/year
Disclaimer: The pricing is subject to change.
Why We Like It
The software stands out for its IRS-compliant e-delivery and e-signatures, which are beneficial for businesses with large 1099 filing needs. It automates the process of validation checks to reduce common filing errors. If year-end reporting for contractors is a pain point, this platform turns it into a streamlined, reliable process.
User Ratings
User feedback mentions that it consolidates all e-file, print, mail, and recipient delivery options. However, some users say that the interface is outdated.
12. Playroll
Playroll is a global workforce management software that offers integrated onboarding, payment, and compliance capabilities. The platform helps businesses streamline 1099 contractor management from a single platform. Additionally, it makes global contractor payroll and compliance easier to handle without manual spreadsheets or fragmented systems.
Pros And Cons
Pros | Cons |
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Best For
Small and medium-sized businesses are looking for a platform that offers contractor management with automated compliance checks.
Key Features
- Employee Portal
- Integrated Analytics
- Review And Approval Workflows
- HR And Finance Integrations
- Unified Payroll Platform
Pricing
Playroll pricing starts at $35/contractor/month for its Contractor Management plan. The vendor offers pricing plans for global payroll services, which include:
- Global Payroll Services - $10/employee/month
- Global Payroll Analytics - $2.07/employee/month
It offers Employer Of Record Services, starting at $399/employee/month.
Disclaimer: The pricing is subject to change.
Why We Like It
Playroll shines due to its centralized invoice management system, which gathers all the contractor’s financial workflows into a single dashboard. It allows contractors to submit invoices and timesheets, which makes it easy for the administration to review, approve, or reject them with full audit trails. This is beneficial for businesses to process all invoices simultaneously, track outstanding payments by contractor, and maintain complete financial visibility.
User Ratings
User reviews appreciate the software because it easily helps prepare and file 1099 forms. Whereas some users say that they faced occasional glitches during peak hours.
13. TimeTrex
TimeTrex offers an all-in-one payroll processing software for businesses managing 1099 employees. It handles direct deposits, check printing from a unified system, easily generates year-end forms that include the 1099-NEC, and automates tax calculations. Moreover, the platform offers built-in compliance tools for customizable deductions, tax filing, and electronic pay stubs. This maintains detailed audit trails for multi-jurisdictional compliance requirements and streamlines contractor payment workflows.
Pros And Cons
Pros | Cons |
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Best For
It is an ideal choice for organizations in the retail, manufacturing, healthcare, and education sectors seeking a platform that offers comprehensive 1099 tax reports.
Key Features
- Employee Database Management
- Payroll Management
- Performance Management
- Applicant Tracking
- Time And Attendance Management
Pricing
TimeTrex pricing starts at $50/month for its Professional Edition plan. Further pricing plans include:
- Corporate Edition - $80/month
- Enterprise Edition - $100/month
Disclaimer: The pricing is subject to change.
Why We Like It
The software stands for its integrated time-to-pay workflows, which eliminate the fragmentation of data while using separate payroll and time tracking tools. It calculates the contractor's working hours through mobile punch and biometric time clocks. It flows directly into the payroll calculations, reducing administrative reconciliation and payment errors. This is well-suited for businesses that manage multiple contractors across various job sites and helps prepare compliant contractor payments.
User Ratings
Based on multiple user reviews, the platform is well-regarding for its accurate time tracking functionality. However, some users note that the platform is complex for first-time users.
Key Buying Advice While Selecting The Best Payroll Software For 1099 Employees
When selecting the best payroll software for 1099 employees, there are certain things to keep in mind.
Look for a self-service portal that allows contractors to update their payment and tax details, track payments, and manage their accounts. Consider payroll platforms that offer audits, tax filing, and labor law compliance features. Additionally, choose platforms that help businesses to deposit wages and salaries electronically. This way, administrators can streamline their tasks while saving time and resources.
It's better to look for tools that generate 1099-MISC and 1099-NEC forms, handle e-filing with the state agencies and IRS, and validate the contractor's information. Furthermore, the software should support integration with accounting tools and project management platforms for seamless data flow.
What Not To Overlook
- Whether the software offer multi-currency support for international contractors
- The software should be able to process bulk payments without any limitations
- Verify that the platform should maintain detailed payment histories for audit trails
- Choose platforms that can flag invalid TINs and handle withholding calculations
The payroll solutions mentioned in this guide excel in their compliance support, contractor-focused automation, and positive user reviews from businesses that manage 1099 employees. These tools are designed to reduce the risk of filing errors, automate payments, and simplify payroll processing. Whether you run a startup, agency, or growing enterprise, the right payroll software for 1099 employees helps you stay compliant, save time, and manage contractor payments with confidence.