9 Best Payroll Software For 1099 Employees

Payroll software helps streamline various organizational and administrative functions, including accurate compensation processing, compliance with legal regulations, and more. While the basics of these operations remain the same, the intricacies and execution vary depending on the business type, nature of employment, and other specifications. 

1099 contractors, for instance, handle their own taxes, requiring a different approach to payroll management. The term '1099 employees' or '1099 contractors' comes from Internal Revenue Service (IRS) Form 1099, which businesses use to report payments made to independent contractors. Unlike W-2 employees, who have taxes withheld from their paychecks by employers, 1099 contractors are responsible for managing their own taxes, including income tax, Social Security, and Medicare. 

The best payroll software for 1099 employees simplifies the payment process, automates tax form generation, and offers flexibility to accommodate varying payment schedules. Given these requirements, we have compiled a list of the best payroll software for 1099 employees so you can streamline finances as efficiently as possible. Keep reading to learn more! 

Top 9 Best Payroll Software For 1099 Employees

Here is a list of the top nine payroll software solutions for 1099 employees, selected based on various factors that will be discussed later in this blog:

  • Gusto HR
  • ADP Workforce Now
  • PrimePay
  • Eddy HR
  • Paycor
  • Bamboo HR
  • Paychex Flex
  • Buddy Punch Time Clock
  • QuickBooks Time Software

    • Comparison Table

    Company 

    Best for 

    Main Features 

    Pricing 

    Gusto HR 

    • Full-service payroll 
    • Federal law compliance 
    • Talent management  
    • Detailed analytics and reporting  
    • Comprehensive time and attendance tracking 

    The pricing starts at $40/person/month 

    ADP Workforce Now 

    • Automated tax calculations 
    • Accurate payroll processing  
    • Benefits administration 
    • Talent acquisition  
    • Central platform for various HR operations 

    Contact us for the pricing 

    PrimePay 

    • Unlimited and automated payroll processing  
    • Efficient time tracking 
    • Employee self-service portal 
    • Applicant tracking 
    • Employee training tracking 
    • Extensive analytics 

    Contact us for the pricing 

    Eddy HR 

    • Integrated platform for multiple tasks 
    • Efficient payroll processing 
    •  
    • Comprehensive employee hiring and onboarding 
    • Accurate time and applicant tracking 
    • Effective payroll management  
    • Workforce documents can be accessed easily 

    The pricing starts at $4/person/month  

    Paycor 

    • Helps drive engagement and boost productivity 
    • Facilitates background screening 
    • Talent acquisition and management  
    • Comprehensive onboarding functionality 
    • CV parsing  

    Get in touch for pricing 

    BambooHR 

    • Manage workforce data efficiently 
    • Automates payroll and wage calculations 
    • Employee onboarding and offboarding 
    • Performance management  
    • Paid time off (PTO) tracking 

    Get a custom price 

    Paychex Flex 

    • Human capital management (HCM) 
    • Accurate time and attendance  
    • Workforce and talent management 
    • Employee self-service 
    • Streamlines HR operations 

    Contact us for a custom quote 

    Buddy Punch Time Clock 

    • Employee scheduling and time tracking  
    • Simplifies payroll  
    • Geofencing  
    • PTO tracking  
    • Photos on punch  
    • Detailed analytics and reporting  

    Starting pricing is $4.99/user/month  

    QuickBooks Time Software 

    • Accurate and timely payroll processing 
    • Efficient time tracking  
    • Billing and budgeting 
    • Project management  
    • Customizable reports  

    Reach out for personalized pricing 

    Gusto HR

    Gusto HR

    One of the most essential human resources (HR) tasks is automating payroll processing, direct deposits, tax filings, and ensuring timely payments. Gusto HR is equipped for all such functionalities and more. It is tailored to serve small and medium-sized businesses and freelance contractors to help them manage their intricate remuneration tasks. The software is easy to navigate, and its intuitiveness streamlines operations across the board, saving time and labor. 

    Unique Features

    Gusto HR is equipped with comprehensive time-tracking functionality, which helps track employees' clock-in and clock-out periods. This further facilitates accurate payroll calculation and lessens the chances of human errors. Additionally, the platform allows users to customize their reports, which further helps produce accurate results.

    Pros

    • Helps comply with labor and wage laws
    • Comprehensive employee onboarding
    • Efficient reports customization

    Cons

    • Customer support can be improved
    • No employee scheduling is available

    Pricing

    The platform offers varying pricing plans, starting at $40/person/month.

    ADP Workforce Now 

    ADP Workforce Now

    The corporate world is progressing at a fast pace, and to keep up with the ever-changing trends, it is essential to be equipped with the latest and most technologically advanced solutions. ADP Workforce Now is a software that leverages extensive insights to streamline HR functions and payroll processing. 

    Unique Features

    Besides providing an efficient applicant tracking system (ATS), ADP Workforce Now also facilitates recruiters and contractors to post jobs across multiple job boards. Additionally, users can create customized job postings to attract well-qualified candidates and simplify the hiring process.

    Pros

    Cons

    • The time-off feature can be improved
    • Some users struggled with the ATS module

    Pricing

    The software offers flexible pricing plans.

    PrimePay

    PrimePay

    If you are looking for software that empowers your workers to access and calculate their wages daily, PrimePay might be what you need. It is also quite helpful in increasing employee satisfaction, engagement, and retention rates. Additionally, users do not have to wait for the next payday to learn about their earned balance, which reduces their financial stress and makes them more productive and mindful. 

    Unique Features

    The software provides a customizable self-service portal that employees can individually access and manage. Moreover, PrimePay facilitates effective time tracking to calculate payroll accurately, further alleviating the burden on the HR team.

    Pros

    • Supports efficient payroll management
    • Comprehensive employee self-service portal
    • Streamlines tax filing and other monetary tasks

    Cons

    • Customer support can be improved
    • The PTO functionality can be more streamlined

    Pricing

    The platform offers multiple pricing plans. Contact us for custom pricing.

    Eddy HR 

    Eddy HR banner

    Organizing workforce data is vital to improving workforce performance as it creates hurdles for the employees and the administrative team. Eddy HR provides swift access to users' profiles, experience, and performance reviews. It is also helpful in auditing and compliance with law. 

    Unique Features

    The platform can be integrated with various job boards that help recruiters hire great talent from diverse backgrounds. Additionally, it offers accurate applicant and time-tracking services, ensuring smooth payroll processing and saving time and resources.

    Pros

    • Customized onboarding process
    • Workforce data can be accessed easily
    • Efficient employees' progress monitoring
    • Comprehensive payroll management

    Cons

    • The license expiration dates should be provided
    • Employee database navigation can be made more intuitive

    Pricing

    The software offers varying pricing plans starting at $4/user/month.

    Paycor 

    Paycor

    Workforce management is a multifaceted task that needs efficient monitoring – something that cannot be executed without thorough insights. Paycor is tailored to meet these specific requirements and more. It provides a centralized system with detailed analytics about the entire workforce, streamlining administrative operations. 

    Unique Features

    The software facilitates comprehensive feedback functionality that helps employers assess their workforce performance. In addition, Paycor is equipped with detailed time management and onboarding functionalities that automate the paperwork associated with the hiring.

    Pros

    • Efficient time management functionality
    • Regular updates help streamline the workflow
    • Great customer support
    • Customizable reporting and analytics

    Cons

    • The mobile app can be made more intuitive
    • The interface can use an upgrade

    Pricing

    The vendor offers personalized pricing plans catering to different business requirements.

    BambooHR 

    BambooHR

    Administrators' and contractors' tasks can often be tedious and time-consuming. The redundancy can be alleviated by incorporating an advanced payroll platform that offers full-suite functionalities. BambooHR Payroll is one such solution that is designed to streamline HR operations. 

    Unique Features

    The software simplifies administrative tasks by providing detailed insights that efficiently encapsulate diverse operations, such as CV parsing, hiring, onboarding, and payroll management. Its pre-built integrations further facilitate the contractors' alignment of the platform with other tools, thereby reducing the burden and saving time.

    Pros

    • Customizable employee self-service portal
    • Helps with detailed background checks
    • Regular updates help users stay ahead of the curve

    Cons

    • The billing feature needs improvement
    • The mobile app can be made more intuitive

    Pricing

    The platform offers tailored pricing plans. Contact us to get a quote.

    Paychex Flex

    Paychex Flex

    Hiring candidates for your firm can be laborious and time-consuming, ultimately calling for a software solution that empowers you to unify diverse tasks. This is where Paychex Flex comes in. From security, scalability, CV parsing, talent acquisition, and timely customer support, it provides all functionalities in a user-friendly way. 

    Unique Features

    The software helps contractors manage payroll while ensuring law compliance. It also helps you track employees' clock-in and clock-out timings, which helps calculate accurate wages. Professional employer organization (PEO) and human capital management (HCM) are other functionalities that help managers wrap up their tasks seamlessly.

    Pros

    • Automated payroll processing to reduce errors
    • Efficient law and tax compliance
    • Extensive reporting and analytics

    Cons

    • The feature upgradation processes can be streamlined
    • Import and export of datasets can be improved

    Pricing

    The platform offers customized pricing plans depending on your business requirements.

    Buddy Punch Time Clock

    Buddy Punch Time Clock

    Time tracking is of great value regarding wage or payroll calculation and tracking. Buddy Punch Time Clock provides online punch-in functionality that helps employees and employers stay on the same page. Users can track their timings, calculate payroll, and track personal time off and overtime. 

    Unique Features

    The software provides built-in notifications that are helpful for accurately measuring time and other payroll computations. The real-time dashboard and automated timesheets help all users across the board to stay compliant.

    Pros

    • Geofencing functionality enables accurate time-tracking
    • Automated timesheets reduce mishaps
    • Customizable workflows enhance work efficiency

    Cons

    • The employee data importing feature can be improved
    • The web portal should be introduced

    Pricing

    The software offers different pricing plans starting at $4.99/user/month.

    QuickBooks Time Software

    QuickBooks

    Track your workforce in real-time by efficient geofencing provided by QuickBooks Time Software. You can also update your time-tracking tasks today with its customizable templates. Monitor your hybrid teams and streamline work operations with great accuracy and convenience. 

    Unique Features

    The software provides a job-tracking functionality that helps you track your workers' accurate working hours. This is particularly beneficial for tracking work progress and calculating accurate payroll.

    Pros

    • Comprehensive reporting and billing feature
    • Mobile app helps track time from anywhere
    • Customizable templates for varying tasks

    Cons

    • The data transfer can be time-consuming
    • The desktop interface can be more intuitive

    Pricing

    The platform offers varying pricing plans depending on the size of your team and your requirements.

    How We Selected The Best Payroll Software For 1099 Employees?

    After reviewing the top payroll software for contract employees, we want to explain how we selected the options listed above. Contractors and freelancers often have diverse work arrangements, so several key factors must be considered when choosing payroll software for 1099 employees. In the following section, we will walk you through various considerations in our selection process.

    Criteria Setting

    Criteria Setting

    We narrowed down our search by looking up software that specifically catered to 1099 employees. Discerning the varying needs of businesses that opt for varying contracts is essential in determining specific platforms for them, as they often differ from the mainstream ones.

    Thorough Evaluation

    Thorough Evaluation

    We analyzed the shortlisted payroll software's basic yet most important features, focusing on payroll processing, onboarding software functionalities, and compliance capabilities. We consolidated our research by delving into user reviews and carefully weighing users' opinions on aspects like interface, navigation, and feature upgrades.

    This thorough approach helped us identify the most effective payroll software for freelance contractors and other non-traditional workers.

    Scalability

    Scalability

    The payroll platform should provide varying pricing plans so recruiters can buy a plan that fits their budget while providing all the essential features. Additionally, it should be able to accommodate an increasing number of employees while retaining its smooth execution.

    Customization

    Customization

    The basic functioning and requirements vary from business to business. Therefore, payroll software should be easily customizable to meet dynamic organizational needs. It should enable contractors to customize reports, payroll, hiring, and onboarding processes as per their requirements.

    What Features To Look For In Payroll Software For 1099 Employees?

    Certain features are essential for any payroll software, especially when managing contractors. Below are the must-have features you should prioritize.

    Law Compliance

    Law Compliance

    Audits, tax filing, deposits, and wage and labor law compliance are some of the most basic and crucial tasks every business must handle. Given how frequently these laws are implemented and followed through, it is vital that payroll software must be equipped with relevant features.

    Direct Deposit

    Direct Deposit

    We live in a technologically advanced world where almost all businesses deposit wages and salaries electronically. This necessitates payment features in global payroll software that can automate payroll processing and save employers’ time and resources. These functionalities include wire transfers, PayPal, and ACH transfers, in addition to a direct deposit feature.

    By scheduling and automating payments on a weekly or monthly basis, administrators can streamline their tasks while saving time and resources.

    Analytics And Reporting

    Analytics And Reporting

    Detailed analytics and reporting help monitor the entire workforce data and calculate salaries accordingly. Therefore, extensive analytics is one functionality in payroll software that you should not forsake.

    Self-Service Portal

    Self Service Portal

    An extensive self-service portal allows contractors to update their payment and tax details, track payments, and manage their accounts. This feature eliminates the need for constant back-and-forth communication, making the payroll process more efficient for both contractors and employers.

    Time And Expense Tracking

    Time And Expense Tracking

    Some companies pay contractors on an hourly basis or reimbursable expenses system, and an efficient billing and time-tracking feature helps monitor all such activities and more. These capabilities help monitor billable hours and expenses, ensuring transparency and accuracy in payments.

    Benefits Of Payroll Software For 1099 Employees

    The benefits of payroll software cannot be glossed over. It helps employers in numerous ways, such as:

    • Payroll software help save time, which is of the utmost importance. Once employers can streamline their basic operations, they can utilize that precious time catering to other tasks
    • Human errors are inevitable, especially in tasks that need micromanagement. Payroll software alleviate the chances of such errors and improve workflow
    • Payroll software are tailored to provide strict security protocols that protect the entire company and its workforce data
    • Most payroll platforms are equipped with diverse geofencing functionality that helps employers track their employees' location and working hours effectively

    FAQs

    Businesses can have different requirements depending on their priorities and the functionalities they lack. Since 1099 employees are not working full-time, they rarely need conventional software. Having said this, employers should look for software that caters to their basic needs. For instance, if most of the freelance employees work on alternate days or have varying working hours throughout the month, employers should choose the platform accordingly.

    QuickBooks is a good software for managing and tracking the financial information of 1099 employees. It eliminates manual data entry and automates various tasks, including budgeting, inventory and time tracking, and bookkeeping.

    Yes, ADP caters to 1099 employees with great speed and accuracy.