The best payroll software for contractors helps you pay and onboard independent contractors and collect the forms you’ll need for end-of-year tax reporting. Many even offer direct deposit at no additional cost, including pricing plans that only charge you during months you process contractor paychecks.
In this guide, we evaluated 15 independent contractor payroll software for small businesses and narrowed it down to our top seven.
- QuickBooks Payroll: Best overall payroll services for independent contractors and those needing a low-cost payment plan
- Square Payroll: Best for retail and restaurant businesses, including Square POS users
- Gusto: Best contractor payroll services with new hire reporting
- OnPay: Best payroll for contractors with only individual taxpayer identification numbers (ITINs)
- Rippling: Best HR, payroll, and IT tools to manage the entire contractor lifecycle
- Deel: Best for flexible global contractor payments
- Remote: Best for indemnity protection against global contractor misclassification
Want to know the differences between contractors and employees? Read our 1099 vs W-2 workers guide.
Best Contractor Payroll Services Compared
Looking for something else? If you want basic HR tools, including the ability to pay both employees and contractors, then check our buyer’s guides on the best online payroll services and best payroll software.
QuickBooks Payroll: Best Overall Contractor Payroll Software
Pros
- Affordable contractor payments plan with next-day direct deposits
- Seamless integration with QuickBooks accounting
- Generates and electronically files year-end contractor tax forms
- Unlimited contractor payments
Cons
- Contractor plan’s 1099 efiling services cost extra (this includes QuickBooks printing and mailing the forms to contractors)
- Doesn’t file new hire reports for contractors
- Limited integration options (of non-Intuit products); requires a QuickBooks Accounting account to unlock full integrations
Expert Opinion
QuickBooks Payroll is our top payroll software for independent contractors because it has the lowest-priced service among the providers we reviewed. It even offers a full-service plan that can handle fast payments for both employees and contractors. And, if you use QuickBooks for accounting, you get seamless data transfers between its payroll and accounting modules, which helps minimize errors from manual data inputs.
The provider earned an overall score of 4.61 out of 5 in our evaluation, with perfect marks in pricing and reporting. However, limited HR tools and third-party software integrations (mostly integrates with QuickBooks products), including the lack of new hire reporting for contractors, cost it some points.
- Contractor payments: $15 monthly for up to 20 contractors (plus $2 for each additional worker)
- For businesses that only pay contract workers
QuickBooks Payroll Plans for Paying Employees and Contractors
- Payroll Core: $45 per month plus $6 per person monthly
- Payroll Premium: $80 per month plus $8 per person monthly
- Payroll Elite: $125 per month plus $10 per person monthly
- Fast direct deposits: QuickBooks Payroll’s contractor payments plan comes with next-day direct deposits—faster than Gusto and Square Payroll’s standard processing timelines (which is four days).
- Contractor self-setup: Contract workers can set up a QuickBooks Payroll account online, enabling them to complete W-9 forms and provide banking information for direct deposit payments.
- Unlimited 1099s and contractor payments: QuickBooks doesn’t place a limit on the number of times you process contractor payments and generate 1099 tax forms. However, you have to pay extra if you want QuickBooks to print and mail the forms to contractors.
- QuickBooks integration: You don’t have to worry about manually downloading and uploading data files from payroll to accounting—data transfers are seamless between QuickBooks products.
Many of the QuickBooks Payroll reviews on third-party sites like G2 and Capterra are about its entire payroll platform and not just contractor payment services. Users like that it is easy to set up and use, with payroll tools that automatically calculate wages, deductions, and payroll taxes.
However, customer support quality is less than ideal, with reviewers complaining of having experienced long wait times. A few users also said that its payroll platform can be pricey for small businesses, while others wished for better reporting capabilities.
Square Payroll: Best for Restaurants, Retail Shops & Businesses Using Square POS
Pros
- Low-cost contractor-only plan with automatic and unlimited pay runs
- Integrates with Square POS and provides free time tracking
- Contractors can self-onboard and view payslips/tax forms via the Square Payroll app
- Preps and files year-end contractor tax reports
- Offers fast direct deposits, including an instant payment option
Cons
- Standard direct deposit has a four-day processing time
- A Square Payment account is needed for next-day direct deposits and instant payments
- Instant contractor payouts are only available if you process both employee and contractor payroll
- New hire reporting services don’t include contractors
Expert Opinion
Square Payroll has solid payroll tools and integrates seamlessly with Square POS, which comes with free time tracking. This is great for retail and restaurant businesses that pay hourly workers. Costing $6 per worker monthly, it’s also an affordable option, especially if you only pay up to two contractors a month. However, for bigger teams, I recommend QuickBooks Payroll, which charges $15 monthly for up to 20 contractors (plus $2 per additional worker).
Overall, Square Payroll earned a score of 4.47 out of 5 in our evaluation. It would have received a higher rating if not for its limited HR features, the lack of new hire contractor reporting, and its standard four-day direct deposit timeline (you need a Square Payments account to unlock instant payments).
- Pay contractors only: $6 per contractor monthly
- For businesses that only pay contract workers
- Pay employees and contractors: $35 per month plus $6 per person monthly
Add-ons
- Mail paper copies of 1099 and W-2 tax forms: $3 per worker annually
- Direct integration with Square POS: Its integration with Square POS means you don’t need to buy a separate time tracking tool to capture contractor work hours. Data transfers of employee tip data are also seamless between Square POS and Square Payroll. Note that the other providers on our list lack direct integration with Square POS (except QuickBooks)
- Unlimited contractor payments: You can pay contractors as many times as you need—Square will only charge you $6 per worker monthly, which is an affordable option for those that only hire up to two contractors a month. It generates 1099-NEC forms at year-end and, like OnPay, mails the paper copies to your contractors for a fee.
- Multiple payment options: Pay contractors through checks and four-day direct deposits. While it offers next-day and instant payments, you need a Square Payments account and have to process both employee and contractor payroll.
- Self-service portal: Aside from receiving pay notifications, contractors can see their payment histories, download tax forms, and update personal information via the Square Team App.
Users who left Square Payroll reviews on G2 and Capterra appreciate its user-friendly platform and helpful time tracking tools. They also like that it streamlines small business payroll processing.
However, a few reviewers said that its contractor payroll is slower than employee pay runs. Some also wish for additional HR features and a more responsive support team.
Gusto: Best Contractor Payroll Service With New Hire Reporting
Pros
- Self-service portal, which contractors can access for a lifetime
- Self-onboarding with electronic W-9 forms
- Preps and files 1099 year-end reports
- Multiple direct deposit options (two-, four-, and next-day payouts)
- Can handle international contractor payments in more than 120 countries
Cons
- Contractor direct deposits follow a four-day processing timeline; Gusto’s other direct deposit options are not available for contractors
- International contractor payments cost extra; requires that you have at least one local contractor added to the “contractor-only” plan
- Limited premade reports
Expert Opinion
Gusto provides all the essential tools you need to manage contractor payments. It prepares and files 1099-NEC reports and lets your new contractors onboard themselves. Gusto also has a special pricing plan for contractors and can handle international payments if you have global contract workers.
With a score of 4.43 out of 5, Gusto would have earned a higher overall rating had it not been for its limited customizability and pricey contractor-only plan—which is more expensive than QuickBooks Payroll ($35 plus $6 per worker monthly vs $15 monthly for 20 contractors plus $2 for each additional worker). You also have to upgrade to its highest tier to get expert advice from certified HR professionals.
- Contractor-only plan: $35 plus $6 per contractor monthly
- For businesses that only pay contract workers
- International contractor payments add-on: Custom-priced
Gusto Plans for Paying Employees and Contractors
- Simple: $40 per month plus $6 per employee monthly
- Plus: $80 per month plus $12 per employee monthly
- Premium: Contact sales
- Automated and unlimited payroll: Gusto offers automatic and unlimited pay runs, even if you’re only processing contractor payments. Payouts are via manual checks and four-day direct deposits. For faster contractor payments, QuickBooks Payroll is a better option given its next-day direct deposits.
- International payroll capabilities: This add-on solution lets Gusto pay contractors in over 120 countries—provided you get either its full-service payroll package or have one domestic worker under its “contractor-only” plan. If you only need to pay international contractors, consider Remote, as it has a reasonably-priced contractor solution with a wider payroll coverage (more than 200 countries).
- Self-service portal for contractors: Contractors can access their pay information and tax forms via Gusto’s self-service portal. It also offers self-onboarding tools and state new hire reporting for contract workers—a functionality the other providers in this list (except Rippling and Deel) don’t offer.
Gusto reviews on G2 and Capterra are mostly positive. Many reviewers highlighted its ease of use and wide range of HR tools as its best features. The common complaint is about its occasional software bugs and the hit-or-miss quality of its customer service.
OnPay: Best Payroll for Contractors Who Only Have ITINs
Pros
- User-friendly interface
- Multiple payment options (direct deposits, pay cards, and manual checks)
- Its system lets you add and pay contractors who only have ITINs (individual tax ID numbers)
Cons
- Access to two- or four-day direct deposits depends on OnPay’s risk assessment
- Limited third-party software integrations
- Lacks a low-cost contractor-only plan
Expert Opinion
OnPay makes paying and hiring contractors easy for business owners. You don’t need to request federal tax and Social Security numbers—you can add independent contractors into its system even if they only have ITINs (individual tax ID numbers). None of the contractor payroll solutions we reviewed have this feature. Online onboarding and full-service payroll solutions are also available, including electronic 1099s for contractors.
Scoring 4.14 out of 5 in our evaluation, OnPay received perfect marks in reporting and ratings of 4 and up in ease of use, HR functionalities, and in our expert review. It lost points because it has qualifying requirements for two-day direct deposits, limited software integration options, and doesn’t offer a contractor-only plan like QuickBooks Payroll, Gusto, Deel, Remote, and Square Payroll do.
- $40 per month plus $6 per employee or contractor monthly
Add-ons
- Print and mail 1099 forms to workers: Contact sales
- Insufficient fees if you can’t cover the cost of a pay run: Contact sales
- Easy contractor system enrollments: OnPay lets you use the contractor’s ITIN to start system enrollment processes and file 1099 forms. Note that you have to require the contractor to complete and submit an affidavit or IRS-approved document for failing to get a valid tax ID.
- Full-service payroll: OnPay offers unlimited payroll, multistate payments, and multiple pay options (such as direct deposits, pay cards, and manual checks). However, unlike the other providers in this guide, you have to undergo a risk assessment to determine eligibility for two- and four-day direct deposits.
- Niche payroll services: OnPay specializes in small business payroll, but it can also handle the pay processing needs of churches, clergies, non-profits, and farms.
A majority of users who left OnPay reviews on G2 and Capterra described it as an efficient payroll tool for small businesses. They raved over its ease of use, competitive pricing, and helpful support team. However, other reviewers wished for additional integration options and a more robust reporting tool.
Rippling: Best All-in-One HR, Payroll & IT Solution for Managing the Contractor Lifecycle
Pros
- Modular HR, payroll, IT, and basic finance solutions; you can select the modules you need
- Payroll capabilities include paying international contractors and employees
- Robust onboarding and offboarding processes—includes managing software access and computer device assignments
- Integrates with 500-plus apps
Cons
- Pricing isn’t all transparent
- Time tracking, benefits administration, HR advisory services, and IT tools are paid add-ons
- You have to purchase its core workforce management platform before you can add other solutions
Expert Opinion
Rippling is great for managing the entire contractor lifecycle given its feature-rich platform, which automates processes for HR, payroll, IT, and basic finance functions. It can handle onboarding, performance reviews, and expense management. Its IT tools can help set up workers’ app access and deploy computer devices. When your contractors have ended their contracts, it can send offboarding documents and revoke computer and software access.
Scoring 4.13 out of 5 in our evaluation, it received ratings of 4 and up in nearly all criteria—except payroll functionalities. While Rippling efficiently handles payments for all types of employees, including those working internationally, it lacks the US contractor-only plan that QuickBooks Payroll, Square Payroll, and Gusto offer. It also only supports payments via direct deposits and manual checks.
- Rippling plan*: $35 per month plus $8 per employee monthly
- Includes Rippling’s core workforce management platform, employee onboarding/offboarding, full-service US payroll, time tracking, and software integrations
Other Per-module Costs*
- App, device, and computer inventory management: $8 per employee monthly
- Includes IT tools to manage business apps and computer provisioning and deprovisioning processes
- Benefits administration: Pricing varies, depending on your insurance broker
- HR help desk: Contact sales
- Real-time compliance updates and email/phone support from HR experts
- Global payroll: $20 per employee or contractor monthly
- Processing global payments for employees or contract workers
- EOR services: $599 per employee monthly
- Full employer of record (EOR) services for paying and hiring international workers
*Pricing is based on a quote we received. Contact Rippling to discuss your requirements and get a custom quote.
- Modular solutions: Rippling lets you select HR, payroll, expense management, and IT modules you need—provided you get its core workforce management platform. However, it can get pricey depending on the module selected. If you need to pay US contract workers, QuickBooks Payroll is more affordable with its contractor payments plan costing only $15 monthly for 20 workers (plus $2 for each additional worker).
- Automatic pay runs with international payroll capabilities: Pay US contractors either by the hour or at a set rate and then send payments through two-day direct deposits and manual checks. Rippling can also handle international contractor payments in over 150 countries (Gusto and Deel only handle contractor payments in more than 100 countries).
- Apps and device management: Rippling lets you assign computers, create online accounts, and manage passwords for business apps directly from its platform. It also has deprovisioning tools to help retrieve and reassign devices, disable app access, and remotely lock and wipe data from company-assigned computers when your contractors leave. This is unlike Deel, which offers global device management via its partner solution, Hofy.
- Integrates with more than 500 apps: You can connect Rippling to a wide variety of solutions, such as accounting, legal, advertising, sales, analytics, customer relationship management, and collaboration tools.
Users who left Rippling reviews on G2 and Capterra said that it is generally easy to set up and has good onboarding, time tracking, scheduling, and payroll features. They also appreciate its integration functions and helpful automation tools.
Others mentioned that its mobile app is not as full-featured as its cloud-based platform. There are also mixed reviews about customer support. Some reviewers commended the support team for their excellent service, while a few users said that they received poor service.
Deel: Best Global Contractor Payroll With Robust Payment Options
Pros
- Global payroll tools in over 100 countries
- User-friendly platform with free access to an HR information system (HRIS), Deel HR
- Assigns a dedicated customer success manager (CSM) to its clients
- Contractor payments via bank transfer, crypto, bitcoin, digital payment processors, and a contractor card
Cons
- Dedicated CSM is not provided to small businesses (only available to enterprises)
- Limited HR features
- Deel HR is only free to companies with less than 200 users
- Global direct deposits take two to seven business days, depending on location
Expert Opinion
While Deel can handle payments for US-based contractors, its online solutions are best for those with plans to expand business operations in other countries. Its EOR services can help you find, hire, and pay employees and contractors in over 150 countries. What I like about Deel is its robust payment options. Aside from bank transfers and a Deel contractor card, you can pay workers via digital payment processors, such as Wise and PayPal, and in Bitcoin or cryptocurrency.
In our evaluation, Deel earned an overall rating of 3.76 out of 5, with high marks (4 and up) in HR features, reporting, and our expert review. It lost points because it has limited integration options and lacks new hire reporting for contractors. Deel’s contractor plan is also more expensive than the other payroll services for contractors we reviewed.
- Contractors: Starts at $49 per contractor monthly
- EOR: Starts at $599 per employee monthly
- EOR services for hiring and paying international employees via Deel-owned local entities
- Global Payroll: Contact sales
- Payroll services for companies that onboard and hire employees through their local entities
- Deel HR: Free for companies with less than 200 employees
- This is Deel’s HR solution for storing employee data and managing your workforce
Add-ons
- Immigration: Contact sales
- Visa and immigration support in 25 countries
- Localized employee benefits: Contact sales
- Background checks: Contact sales
- Multiple payment options: Deel offers up to 15 ways to pay global contractors. It can send payments via bank transfer, Revolut, PayPal, Wise, Payoneer, Coinbase, and Binance, among others. None of the other contractor payroll services on our list have this many payment methods.
- Deel contractor card: This is similar to a debit card and allows contractors to spend their earnings securely through in-store or online transactions. Workers can also opt to keep the funds on their Deel card for as long as they want. However, it only accepts the USD currency and, as of this writing, is available only in Argentina, Colombia, Georgia, Mexico, Nigeria, Pakistan, Peru, Philippines, Serbia, Turkey, the United Kingdom, and the US.
- Dedicated support: Deel’s new clients get dedicated CSMs to help them with the initial system setup and serve as the point person whenever they have problems with their accounts. While this is only offered to large companies, small businesses get multi-channel support, such as via email, Slack, WhatsApp, and 24/7 in-app chat.
Deel reviews on G2 and Capterra are mostly positive. Users love its intuitive and user-friendly interface, helpful onboarding tools, and efficient global payment processes. Some also said that its live chat support team is helpful and generally quick to respond. On the other hand, several reviewers mentioned that its solutions and services can get pricey, especially if you have a small team.
Remote: Best for Global Contractor Misclassification Protection
Pros
- Reasonably priced contractor management plan with indemnity protection against worker misclassification
- One-click contractor payments and fee-free local currency payouts
- Offers global job posting tools
- Free HRIS for companies with local entities in countries outside of the US
Cons
- Payments through credit cards have extra charges
- Only generates 1099 forms for US contractors
- Free trial isn’t offered in other plans (like Remote Talent, Employer of Record, and Global Payroll)
Expert Opinion
Remote provides international HR and payroll services, including a full-service EOR option to help you hire international employees. For those with global contractors, it has contractor management solutions that simplify onboarding and payment processes. While it offers worker misclassification tools, Remote takes it a step further with an indemnity coverage of up to $1 million per client.
Scoring 3.53 out of 5 in our evaluation, Remote earned ratings for 4 and up in reporting, HR features, pricing, and our expert review. It has efficient contractor payment tools but scored the lowest in payroll features because it only generates 1099 forms and payments via credit cards have a 3% service fee. Remote also lacks phone and chat support—if you need assistance, you can either check its online help center or contact its support team via email.
- Contractor Management: $29 per contractor monthly; payments made through credit cards have a 3% service fee
- Contractor Management Plus: $99 per contractor monthly
- Contractor Management features + indemnity protection against worker misclassification
Remote Plans for Employees
- HRIS: Free software for storing employee data, onboarding and offboarding workers, and more
- No employee limits; only for companies that have local entities
- Employer of Record: Starts at $599 per employee monthly
- EOR services to help you hire and pay international employees
- Global payroll: Contact sales
- Includes payroll services, invention and IP rights protection, and legal compliance management
- Remote Talent: Starts at $199 per month
- Job posting and hiring solutions for attracting global employees
- Efficient contractor management tools: This solution comes with contractor invoicing, automated approvals, and built-in security to protect your invention and intellectual property rights. What’s also unique about Remote is its indemnity protection, which covers penalties, fines, and damages due to worker misclassification (up to $100,000 per contractor and $1 million per client).
- One-click contractor payments: Invoices that contractors send will appear automatically in your Remote dashboard. You can approve invoices with one click and even set up automatic approvals for specific transactions. Remote then distributes the approved payments to the contractors’ accounts either through direct deposit (processing timelines range from two to nine days) or via credit card (this comes with a 3% service charge).
- Local currency payouts but with simplified billing: Remote supports payments in more than 200 countries and over 70 currencies. Note, however, that the contractor billing statements you’ll receive from Remote won’t be in different currencies. You will be charged in the currency that both you and Remote agreed on, which is indicated in your agreement with the provider.
Users who left Remote reviews on G2 and Capterra appreciate that it is simple and easy to use, with a support team that’s helpful and reliable. They added that it simplifies global payroll, hiring, and compliance. However, some users said that it can get pricey to use.
How We Evaluated the Best Contractor Payroll Services
To find the best payroll software for contractors, we used a scoring rubric designed specifically to evaluate payroll software for independent contractors. We looked for features like automatic pay runs, direct deposits, and year-end 1099 reporting. We also compared each system’s ease of use, pricing, customer support, and online user reviews.
To see our full evaluation criteria, click through the tabs on the box below.
25% of Overall Score
Having a direct deposit option with a quick turnaround (two days) plus 1099 form preparation and delivery were most important. Payroll solutions with the capability to pay employees, aside from contractors, were also given an additional point.
25% of Overall Score
Services with contractor-specific plans were rated more favorably (they’re cheaper and more flexible), including those that have transparent pricing and charge you a low rate altogether.
20% of Overall Score
Small businesses need payroll software that integrates with common third-party software, such as time tracking providers. In addition to having an intuitive interface, providers with how-to guides and phone support that’s easy to access were rated favorably.
15% of Overall Score
Online onboarding, which means giving contractors the option to fill out onboarding forms like the W-9 electronically, is the top criterion; following closely behind is the ability to offer a self-service portal that contractors can use to see payments made, edit W-9 information, and print 1099 forms.
10% of Overall Score
In this criterion, we use our expert opinion to assess whether the software’s ease of use, and the width and depth of its payroll and HR tools, are ideal for small business owners. We also evaluated each system’s popularity based on feedback that users left on third-party review sites, such as G2 and Capterra.
5% of Overall Score
Software with basic payroll reports were rated favorably. We also gave extra points to those that offer report customization.
*Percentages of overall score
Regardless of whether you’re getting new contractor payment services or planning to switch payroll providers, you have to consider several factors. The list can be extensive but below are some of the important ones you should look into.
- Business size and location: Your business size and location can help determine your pay processing needs. A provider that handles US contractor payments is best if you only require payroll for 1099 employees. For international contract workers, you need global payroll services, such as those on our list of international payroll software.
- Budget and pricing: Consider payroll companies that offer pricing plans for only paying contractors. These are usually lower than employee payroll packages and can help you save money. Don’t forget to ask if there are add-on fees for system setup, 1099 form printing and mailing services, and HR support.
- Features: Contractor payroll services with automatic pay calculations and built-in payroll compliances can make your life much easier. You’ll also want to evaluate how it handles onboarding, as well as W-9 forms and 1099s—does it help prepare and file them?
- User interface: Look for a payroll system that is simple to learn and use, for both you and your workers.
- Integration options: Consider providers with robust payroll software integrations. This allows you to connect the payroll system with third-party solutions for tracking time, managing accounting, and more.
- Customer support: 24/7 customer support is ideal, but if it isn’t available, look for phone support. You should also check user reviews on third-party review sites for feedback about customer service quality.
Bottom Line
When finding the right payroll solution for contractors, look for online payroll services that can automate and simplify pay processing. It should also come with a price point that won’t break the bank.
We found that QuickBooks Payroll offers the best contractor payment features at a budget-friendly price. Its contractor plan comes with next-day direct deposits and ensures you stay compliant with tax reporting regulations. It even seamlessly integrates with QuickBooks Online Accounting, making it easy for you to update your general ledger for contractor payments.
Sign up for a QuickBooks Payroll plan today.