Best Payroll Software for 1099 Contractors

As your business grows beyond a few team members or if your structure involves a foreign LLC with U.S.-based workers, you’ll probably hire independent contractors. In fact, 11.9 million workers in the U.S. are independent contractors.¹ By default, businesses that hire these workers also need payroll software for 1099 contractors to compensate them.

Your focus needs to be on tools that fit small teams but offer dependable tax documentation and payment tracking. The good news is that there are quite a few options in the market for software that manages payroll taxes. However, the bad news is that it can be tricky to find the right option.

That’s why we’ve created a guide covering 10 of the best payroll software for 1099 employees, all of which are compatible with U.S. contractor rules. Let’s discuss their features below to help you make a pick. We'll also discuss how BatchTransfer can help you do international payroll at the mid-market exchange rate.

10 Best Payroll Software for 1099 Contractors

When you pay 1099 contractors, you have to make sure the payments are accurate and the tax forms are ready when they’re due. The right software for managing payroll taxes will save you all this hassle. Let’s look at a few software options to manage contractor payroll.

1. QuickBooks Payroll

QuickBooks Payroll can handle the full payment process for both employees and independent contractors. It offers a combination of payroll automation, tax filing services and time-tracking features, all in the same ecosystem.

The system can generate and file forms, process same-day direct deposits and maintain detailed payment records for the tax season for independent contractors. You can also connect payroll with bookkeeping to reduce manual entry and cut down on payroll prep time.

Key Features

• HR Support Tools: Teams get access to certified HR advisors for compliance guidance and policy setup.
• Self-Service: QuickBooks Workforce app allows team members to view pay stubs, W-2s and time entries.
• Automatic Payroll Runs: You can schedule payroll in advance to process without manual intervention.
• Time Tracking Integration: It has a built-in connection with QuickBooks Time to approve hours and improve payment accuracy.

Pricing

Plans start at $88 per month with an additional $6.50 per employee per month. The Premium Plan is $203 per month with an extra $10 per employee.²

2. BambooHR

Bamboo HR provides an all-in-one platform that merges payroll, HR data, benefits and employee performance into one organized system. The platform supports accurate payment processing and compliance for multi-state taxation.

Besides payroll, Bamboo HR also offers applicant tracking, onboarding, benefits administration and performance management. The reporting features allow managers to generate pre-built and custom reports to identify trends and track costs.

Key Features

• Time Tracking and Attendance: The platform tracks hours worked and manages multiple pay rates.
• Performance Management: You can set goals, schedule reviews and collect feedback on the platform.
• Custom Dashboards: Teams can access advanced insights and HR benchmarks for better decision-making.
• Employee Self-Service: Staff can access payroll details and request time off themselves.

Pricing

Three plans are available; pricing is provided upon request.

3. Rippling

Rippling brings payroll, HR, IT and expense management together in one integrated platform. It’s suitable for businesses that want a single system to handle both employee and contractor payroll.

The platform automates payment runs and files the correct forms for independent contractors. It also supports compliance in all 50 U.S. states and more than 185 countries.³

Key Features

• Global Payments: Besides the U.S., you can pay contractors in more than 185 countries with built-in local compliance and currency conversion.
• Applicant Tracking: You can post jobs, manage candidates and automate onboarding paperwork to speed up contractor setup.
• Expense Tracking: Rippling automates expense submissions and reimbursements for contractors and employees.
• Custom Workflow Automation: You can build no-code workflows for repetitive admin tasks.

Pricing

Pricing is available upon request.

4. Wingspan

Wingspan is specifically built for businesses that rely heavily on contractors. It covers the entire 1099 contractor lifecycle, including onboarding, verification, payments, compliance and benefits.

The platform further automates key workflows like W-9 collection and invoice processing. It also offers same-day or rapid payments to help companies improve contractor retention.

Key Features

• Automated Invoicing and Payments: Teams can generate, approve and pay contractor invoices with ACH, debit card and other supported methods.
• 1099 Filing: You can automatically prepare and file 1099 forms to reduce the risk of compliance penalties.
• International Contractor Payments: The platform supports international payments with currency conversions.
• Contractor Help Desk: You can provide a centralized support channel for contractor inquiries to reduce admin workload, along with running optional screenings directly from the platform for added trust.

Pricing

Three plans are available; pricing is offered upon request.

5. Patriot Payroll

Patriot Payroll is suitable for small to midsize businesses looking for a simple way to run payroll. It offers Basic Payroll, where you handle tax filings yourself, and Full Service Payroll, which automates all tax deposits and filings for you.

The unlimited payroll runs, free direct deposits and optional integrations for time tracking, HR and accounting make Patriot an excellent option to manage contractor payroll.

Key Features

• Unlimited Payroll Runs: Businesses can process payroll as often as needed without additional fees.
• Employee Self-Service Portal: Team members can view tax forms, pay stubs and update withholding online.
• Built-in Accounting Integration: Patriot’s accounting software helps teams sync payroll data automatically.
• Time and Attendance Integration: The platform helps track employee hours, clock-ins and outs and customer overtime rules.

Pricing

Plans start at $17 per month for Basic Payroll and $37 per month for Full Service Payroll. A free 30-day trial is available.⁴

6. Wave Payroll

Wave Payroll provides an affordable way for small businesses to pay independent contractors, with the option to also handle tax filings in select U.S. states. The platform integrates with Wave’s free accounting software, so you can sync payroll data with your books.

Some other notable features of Wave include time-off tracking, automated tax filing, self-service portal, leaves and benefits support and flexible payment options.

Key Features

• Unlimited Direct Depots: You can transfer funds securely to contractors’ bank accounts at no extra cost.
• Self-Service Portal: Workers can access their year-end tax forms and update personal or banking information themselves.
• Expense and Tax Reports: Payroll teams can generate payroll expense summaries and tax payment reports to get a view into costs.
• Time-Off Tracking: The platform supports tracking of vacations, sick leaves and accruals directly in the payroll system.

Pricing

A basic free plan is available. Paid plans start at $16 per month, or billed annually at $170.⁵

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Pay Employees With BatchTransfer

BatchTransfer has an easy-to-use instant payments system that allows you to make multiple payments, for both domestic and international, in one go. Small businesses and enterprises can get access to BatchTransfer with no additional cost after getting a Wise Business account.

BatchTransfer’s core strengths for payroll:

What sets BatchTransfer apart is its commitment to providing the mid-market rate for currency conversions. This means that businesses get a fair and transparent deal when making international payments.

Another perk of using BatchTransfer for international payroll is its extensive coverage of over countries and currencies! With features like automatic payment scheduling and API integration, small businesses can streamline their payroll process, freeing up valuable time and resources for other important tasks.

• How can businesses use BatchTransfer for payroll?: Businesses can send up to 1000 payments with a single click with BatchTransfer. US-based business can access BatchTransfer at no extra charge.

• Connect to your accounting software: You can easily manage and reconcile your mass payments through accounting software integrations such as QuickBooks or Xero.

Start making payments
with BatchTransfer >>

Wise Features	Price
Mid-market exchange rate for currency conversions Payments to countries in currencies Delivery estimator, real-time tracking, pay-to-email & more	Free to sign up for US business accounts, no monthly fees, no minimum balance requirements. Transparent and competitive rates Free access to API, BatchTransfer, and integrations features. You can also get major currency account details for a one-off fee to receive overseas payments.

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7. Square Payroll

Square Payroll, with its POS integration and full-service tax filing, makes paying independent contractors a breeze. It can automatically pull in hours and commissions so you can process payroll in minutes.

Plus, its built-in features include tax filing, compliance support and benefits management. The pricing is also quite affordable for small businesses trying to scale.

Key Features

• POS Integration: Teams can automatically import timecards, tips and commissions from Square POS to reduce manual entry.
• Accounting Sync: The platform connects with QuickBooks Online for automatic bookkeeping updates.
• Multi-Pay Rate Support: You can pay contractors with different rates for tips or job types.
• Mobile Payroll Management: Square lets you run payroll from anywhere via the Square Team App.

Pricing

A free plan is available. Paid plans range from $49 to $149 per month. Custom pricing is also available upon request.⁶

8. RemoFirst

RemoFirst is a global employer of record (EOR) and payroll solution that makes hiring and managing talent cost-effective and compliant in 185 countries. That means you can manage international contractors with ease.

The platform also removes the complexity of setting up entities abroad. It also keeps you compliant with local labor laws.

Key Features

• Automated Global Payroll: The platform can handle multiple currencies and tax deductions across the world.
• Dedicated Account Manager: You can receive personalized assistance for onboarding and HR strategy.
• Workforce Management Tools: RemoFirst centralizes HR processes, including background checks, document storage and visa or work permit support.
• Fast Onboarding: You can get employees or contractors set up quickly with minimal paperwork and 24/5 customer support.

Pricing

A free plan is available for contractor management. Paid plans start at $25 per person per month.⁷

9. Plane

Plane is an all-in-one platform for managing global payroll, HR and compliance. It helps businesses hire, pay and manage people in more than 240 countries without juggling multiple tools.

The platform’s automation and transparent pricing make it suitable for growing businesses. Plus, the hands-on support takes the heavy admin work off your plate.

Key Features

• EOR in 100+ Countries: The platform lets you hire international employees in days without setting up local entities, while staying compliant with labor laws.
• HRIS for Entire Team: You can centralize onboarding, PTO tracking and reporting for all workers.
• Local Compliance Expertise: Teams can access country-specific legal guidance on employment laws and tax rules.
• US W-2 Payroll: You can run compliant multi-state payroll for US contractors, including tax form processing.

Pricing

The Contractor plan costs $39 per month.⁸

10. Paycor

Paycor is one of the best payroll software for 1099 contractors in companies that want automation and complexity. The platform has been available for more than 30 years and has innovated immensely.⁹

It offers tools to pay employees and contractors accurately while keeping up with changing tax regulations. The mobile-friendly interface and proactive compliance alerts make it appealing for organizations with distributed teams.

Key Features

• AutoRun Payroll: Teams can schedule payroll to process automatically at a chosen time without logging in.
• Tax Guidance and Filing: You get location-based tax setup recommendations and have Paycor handle W-2, 1099 and other filings for you.
• Direct Deposits and Pay Cards: The platform lets you eliminate paper checks with direct deposits or funds loaded to a Paycor Visa Card.
• Employee Self-Service: You can give staff mobile access to pay stubs, W-2s, benefits and time-off balances.

Pricing

Pricing is available upon request.

Frequently Asked Questions

Can payroll software automatically file 1099 forms?

Most modern payroll platforms can automatically generate and file 1099-NEC forms with the IRS. They also provide copies to your contractors electronically or by mail.

Can payroll software pay international contractors?

Yes, but not all payroll tools offer this feature. Platforms like Rippling and Remofirst allow you to pay contractors in over 100 countries. They can also handle currency conversion, tax compliance and local regulations.

What features should I look for in a payroll software for 1099 contractors?

Some features to look for include automated 1099 form generation, flexible payment methods, time tracking, expense management and multi-state or international payment support. It also helps if the tool integrates with your accounting system. Other notable features include strong reporting tools, mobile access and compliance tracking.

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Sources:

1. BLS - Contingent and Alternative Employment Arrangements Summary
2. QuickBooks - Run Payroll
3. Rippling
4. Patriot Payroll
5. Wave Payroll
6. Square Payroll
7. RemoFirst