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 

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 

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 

  • Extensive features to streamline HR operations 
  • Comprehensive reports customization  
  • Efficient payroll management 

Cons 

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

Pricing 

The software offers flexible pricing plans.

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 

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 

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 

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 

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 

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 

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

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

We analyzed the basic yet most important features of the shortlisted payroll software, such as payroll processing, onboarding functionalities, and compliance capabilities. We consolidated our research by sifting through the user reviews and weighing users’ opinions, especially about the interface, navigation, and features upgrade.

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

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

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

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

We live in a technologically advanced world where almost all businesses deposit wages and salaries electronically. This necessitates payment features 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

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

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

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

What to look for in payroll software for 1099 employees?

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.

Is QuickBooks good for 1099 employees?

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.

Does ADP have support for 1099 employees?

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