Find 43 Best Payroll Software with Deductions Management in June 2026

What is Patriot Payroll?

The Patriot's secure payroll solution is designed to lower the total cost of payroll administration, while helping you reduce your staffs' workload. With its fully integrated interface with Patriot's fund accounting and other core compliance solutions, Patriot Payroll Software automates the ...

What is Paychex Flex?

Paychex Flex is a cloud-based payroll software for mid- to large-sized employers, delivering the tools you need to run your business and support your people. This payroll system provides everything you need in just one simple package. It includes: W-2 and 1099 printing, Payroll processing, ...

What is Paycom?

Paycom revolutionizes HR and payroll with fully automated, employee-first technology. Our single database ensures a seamless flow of employee data, enabling streamlined management of the entire employee life cycle.

What is Gusto?

Gusto is a comprehensive HR platform designed to help businesses of all sizes thrive. Whether you’re just starting out or scaling rapidly, Gusto provides the tools and guidance you need to grow and nurture your team. Trusted by over 300,000 businesses across the U.S., Gusto combines payroll, ...

What is Zenefits?

Zenefits Payroll handles all your company's payroll needs. The software is automatically updated with payroll tax tables, so there's no need for you to manually file quarterly updates. Zenefits helps you manage employees, and ensure you're compliant with all applicable payroll laws.

What is Remote.com?

Remote.com is a remote work management platform that simplifies global payroll, compliance, and workforce administration for businesses of all sizes. It seamlessly integrates with HR systems, centralizing payroll data for security and accuracy. The platform enables effortless onboarding with ...

What is OnPay?

OnPay is an intuitive online payroll software designed to meet the needs of supervisors, managers, payroll specialists and people who manage pay for hourly or salaried staff. OnPay helps companies of all sizes reduce costs for processing payroll checks, making tax reports, tracking down pay ...

What is QuickBooks Payroll?

QuickBooks Payroll makes it easy to stay on top of your HR needs. It’s payroll software that gives you the power to handle all the payroll processing you need, from modeling an employee’s paycheck to tracking deductions and taxes. Whether you need a few employees or thousands, QuickBooks ...

What is Justworks?

Justworks is payroll software that offers international payroll, payroll tax filing and realtime benefits administration. The Justworks app is a simple way for teams to bill their hours directly from their iPhone or Android devices. This mobile solution provides employees with a transparent ...

What is SurePayroll?

SurePayroll is a cloud-based, Payroll Software with Time Tracking Service. The software can be accessed from any device and is hosted by SurePayroll in the Amazon Web Services (AWS) data center for fast processing and performance.It automates most employee related tasks including accurate and ...

What is greytHR?

greytHR is a web-based HR software that allows multiple firms to share and manage payrolls in one place. You can access your payroll information from anywhere, anytime using a PC or Smartphone and reduce your costs by avoiding duplicate work and paying for only what you need.

What is ThePayStubs?

ThePayStubs is the best way to quickly generate online pay stubs. Instantly print or access pay stubs to help keep track of salary, taxes, and overtime pay. Get all the info you need about your earnings and deductions with this simple, fast and secure check stub creator. Enjoy stress-free ...

What is Square Payroll?

Square Payroll is our new, easy-to-use payroll software that integrates with your existing payroll provider. It helps you pay employees faster, keep better track of hours worked, and outsource the labor-intensive parts of running a business.

What is Papaya Global?

Papaya Global is a cloud-based payroll management software designed for multinational businesses. It offers a variety of essential features such as data security, cost breakdown analysis, records management, and benefits administration. This integrative platform allows businesses to streamline ...

What is APS Payroll?

APS Payroll provides the functionality, precision, and security you need to help you manage your payroll. It is an easy-to-use yet robust system that meets the needs of even the most complex organizations while delivering accurate and secure paychecks in a timely manner.

What is Microkeeper?

Microkeeper is a user-friendly payroll software that connects you with the world of business payroll processing: delivering quick online setup, automated time keeping and more. Payroll processing has never been easier or more affordable. Microkeeper gives you simplicity and convenience in ...

What is Heartland Payroll?

Heartland Payroll is a payroll management software for small and medium sized companies. It handles all your payroll processing requirements such as bi-weekly, monthly or yearly paychecks, cost accounting and tracking of leave balances. The system has complete comprehensive accounting module ...

What is RUN Powered by ADP?

RUN Powered by ADP (formerly Buildium) payroll software is payroll software that makes payroll accounting easy and affordable for companies of all sizes. With RUN, you gain a comprehensive payroll solution that saves time and saves money.

What is Paylocity Web Pay?

Paylocity Web Pay is a cloud-based payroll software that helps businesses reduce time spent on managing payroll and effortlessly process employee information. The system offers features like time and attendance tracking, unlimited employee data, automated deduction data and a variety of direct ...

What is Paybooks?

Paybooks is a robust payroll software solution that fits the complete payroll needs of you organization. The system is customizable to support multiple companies and tax jurisdictions, and can be deployed either on a local network or hosted in the cloud.