Top 15 Payroll Software for Startups for 2024

Starting a new business can be exciting but also overwhelming, with payroll being a major contributor to the stress, according to one survey. Almost a quarter of the small businesses and startups polled spend four hours or more per week on payroll alone. The big question is, what about the other requirements that startups must meet? This is where payroll software for startups comes in handy.

According to Forbes, a startup faces numerous challenges, such as identifying problems and developing solutions, securing funding, hiring the right people and creating a healthy culture, and achieving work-life balance. Imagine being able to free your hands from doing payroll manually by automating it with payroll software: you’ll be able to focus on other critical tasks that will help your startup grow faster.

If you want to be free of mundane payroll tasks while still ensuring you pay your employees accurately and on time and adhering to government regulations, this list of the top 15 payroll software for startups will assist you in making an informed decision. There will be software to meet your needs regardless of your business type.

Payroll software aids in compliance management, and this becomes significant when you think that only 36% of businesses are familiar with the Federal Insurance Contributions Act (FICA), which requires tax contributions for Social Security and Medicare. Noncompliance issues can cast a negative light on a startup, or any company for that matter.

More importantly, payroll errors are unacceptable because, according to the American Payroll Association (APA), 65% of workers rely solely on their paychecks to survive, and 49% start looking for a new job after two pay errors. Fast employee turnover would be counterintuitive for startups aiming to hire the right people and foster a positive workplace culture. The best payroll software for startups would clearly allow for compliance, not to mention improved workplace relationships.

Payroll management systems are in high demand these days, and many vendors offer software with varying features. Even if you are already convinced that payroll software is ideal for your startup, it is recommended that you consider the following five questions to ask prospective vendors:

• Will my payroll taxes be correctly and timely filed?
• What if I get a notice about my payroll taxes?
• What is the typical timeframe for payroll processing?
• Is it required that I sign a contract?
• How quick is your customer service?

These questions will help you crosscheck the components of payroll software with your startup needs, thus helping you narrow down your options and avoiding getting overwhelmed by the many features that payroll software offers.

Best 15 Payroll Software for Startups 2025

1. QuickBooks Payroll

QuickBooks Payroll is intended for businesses of all sizes, regardless their location around the world. It aims to help you organize your funds, track your cash flow in real-time, and keep you informed about the financial health of your company. It also has sophisticated payroll management capabilities that simplify the process of preparing, filing, and distributing paychecks.

QuickBooks has features that are simple to use for both novice and professional users. It also includes everything you need to run your payroll correctly and on time. Simply enter your rate, employee hours, and commissions, and the app will even calculate tax rates for you. It can print paychecks or deposit funds directly into employee bank accounts and has built-in pay distribution options, not to mention free same-day direct deposit, which eliminates paycheck delays. All of these features cut the time you normally spend on processing payroll in half, allowing you to focus on other aspects of your business.

Furthermore, QuickBooks allows you to sync your payroll and accounting data for real-time adjustments, as well as share files with business partners, consultants, or accountants. It is also mobile-friendly, allowing you to check your payroll and make payments while you are on the go. You can use any browser or mobile application to access the platform’s capabilities. This smartphone app not only allows you to pay your taxes electronically but also sends you automatic reminders about tax deadlines and paydays.

QuickBooks Payroll works with other QuickBooks editions as well as other Intuit industry-specific solutions. It is available in various pricing plans based on the tools you require, and all plans include robust payroll management options as well as user-friendly financial management tools. You can start with the Simple Start plan at $12.50 per month.

2. Gusto

Gusto is an online HR service solution for small businesses that’s designed to simplify complex business operations such as HR, benefits, and payroll. It, therefore, streamlines payroll, benefits, and HR operations with powerful payroll tools, a user interface that is easy to use, and innovative and automated functions. Aside from that, you can use it at a low cost.

Gusto automates your payroll, including not only workers’ compensation but also 401(k) and health insurance. It can file payroll taxes at any level of government while also simplifying year-end paperwork. You can schedule and set up payments, and the system will handle the rest, allowing you to pay employees on time. Your employees can even set up accounts that will allow them to donate directly from their paychecks. All of these procedure are carried out without the use of paper, instead, relying on digital paystubs.

The system will automatically examine data, generate compliance inspections of your benefits, and send automated notices, while also ensuring employee privacy. Furthermore, Gusto consolidates all employee data, from emergency contacts to new hire documentation to anniversaries, allowing employees to access, amend, or download information as needed. This helps you to comply with HIPAA regulations while also making HR management more visible.

Gusto is a flexible platform because of its integration with popular accounting systems like Xero, QuickBooks, FreshBooks, Bamboo HR, When I Work, and Receipt Bank. It offers a one-month free trial after your first payroll. The plans, on the other hand, begin at $39 per month plus, $6 per person for full-service payroll, with no long-term contract required. You can also choose to opt out at any time.

3. OnPay

OnPay easily belongs to our list of top payroll software for startups. It is a complete cloud-based software solution for small and medium-sized businesses that automates payroll, tax filing, and payment routines. Payroll data such as hours, tips, reimbursements, and bonuses, as well as health insurance, 401(k), and workers’ compensation insurance, are easily entered for pay-as-you-go employees.

Furthermore, it handles unlimited payroll runs for W-2 employees and 1099 contract workers on a weekly basis. You can pay your employees by check or direct deposit. Direct deposits are available to those who apply and pass OnPay’s risk assessment. Also, the software’s unlimited pay runs are a valuable feature. The goal is for you to be able to complete payrolls as planned without incurring additional fees. Corrections and pay runs are both cancellable.

OnPay

Try out OnPay with their free trial

Employee self-onboarding and online access, on the other hand, allow employees to enter, edit, and retrieve their own personal data. Your employees’ data is saved in a vault, eliminating the need for time-consuming data entry and allowing employees to view their pay stubs and W-2 forms online even if they are no longer employed by you. This frees up time for more important tasks. The program includes a new hire checklist and alerts you to government reporting and documentation requirements.

One of OnPay’s assets is its simplicity, which allows it to deliver essential functions quickly and effectively. Its simple UI, which includes only the essential tools, reflects this. It also seamlessly integrates with leading accounting, HR, and timekeeping software such as QuickBooks, TSheets, America’s Best 401k, and ThinkHR, among others. Finally, it saves money by bundling services based on the number of employees. The basic plan starts at $40, and you can try it out for free first.

4. Rippling

Rippling is an HR and IT platform that manages payroll, benefits, apps, and devices all in one place. It can automate tasks such as payroll updates, paper management, and app development by bringing everything together on a single platform. Because Rippling integrates with all employee management systems, manual tasks such as salary proration, 401k and tax deduction, and benefit allocation are automated.

Rippling also provides powerful reporting tools, including critical workforce analytics such as employee attrition and compensation trends, as well as productivity metrics such as app usage. This feature aids in the streamlining of workflows. For example, you can create tasks automatically for each stage of the onboarding process. You can send the necessary paperwork to new hires, who must sign it before you can approve it—no more back and forth emails. Employee documents are also kept safe on the platform.

You can monitor salary trends over time, track app usage and identify productivity issues. Your employees can also use the mobile app to view pay stubs, get contact information for coworkers, and request PTO. These features enable employees to work even when they are not physically present at the workplace.

The Rippling platform integrates with over 500 third-party apps, including Slack, Zoom, and Office 365, to ensure that it adapts seamlessly to the app ecosystem that businesses already use, preventing productivity disruptions. Employee hours can also be tracked and imported using apps such as TSheets and When I Work. The software package begins at $8 per month for each user.

5. Trolley

Trolley is a global payments platform that automates payments to sellers and service providers worldwide. Any business can use it to automate payout procedures and send large amounts of money to over 200 countries and regions around the world.

The main advantage of Trolley is that it enables businesses to set up and automate customized payout approvals. Trolley can also be used by businesses to collect and complete IRS tax documents, generate year-end reports, and validate TINs. It also automatically changes withholdings and has robust security measures in place to protect organizations and their suppliers from risk and fraud.

The platform assists businesses in meeting federal and local payment requirements. Payment recipients can also be checked against global watchlists automatically. Additional financial security is provided by 2FA, user roles, and permissions. It also automates payments to suppliers, distributors, and contractors, as well as payment tracking and refund handling.

Trolley works seamlessly with third-party accounting, ecommerce, and CRM platforms to improve business workflows. Xero, Twilio, Asana, Trello, and Google Sheets are examples of such applications. Trolley has three paid pricing plans that range from $49 per month to custom pricing.

6. Xero

Xero is a financial management app designed to help small and medium-sized businesses (SMBs) grow. Its powerful, elegantly designed dashboard provides you with a commanding view of your bookkeeping practice’s clients, jobs, inquiries, and alerts. Meanwhile, you can access client information and actions with a single click, and you can request any document you require from your clients. You can even conduct a client discovery review to learn about their banks, industries, and applications, allowing you to plan ahead for smooth transactions.

Xero is easy to use and maintain, so you can start using it right away. It helps transform some of the most complex and common financial topics into a fun adventure for non-expert consumers. Furthermore, recognizing that businesses require a variety of tools to achieve their objectives, Xero has created a robust app ecosystem around which clients can build their own custom business toolkits. As a result, you can conduct business without breaking a sweat.

Xero is also secure. Its multiple-approval process and two-factor authentication help to reduce financial fraud, and each transaction would include a detailed action list that requires dates, users, and manual remarks. Meanwhile, Xero connects to your bank to receive bank feeds, allowing you to view and track bank transactions. Financial reporting is one of Xero’s best features, allowing you to see the results of all your actions simply by filling out the filters.

Xero integrates with a variety of third-party apps, as well as payment platforms such as Paypal and Stripe, to manage payments for you. It has three pricing plans based on your company’s needs, starting at $5.50 per month.

7. Sage 50cloud Payroll

Sage 50cloud Payroll is a payroll solution for small and medium-sized businesses in the United Kingdom. While it is primarily concerned with payroll, it provides much more, including data collection, employee engagement, and automation of routine operations. It has been approved by HMRC and ensures compliance.

Sage 50cloud Payroll calculates tax deductions and student loans automatically and stores employee data and documents in the cloud. The platform also serves as a shared system for accessing payroll documents by management and employees.

It is also adaptable to unusual circumstances. You can change your employees’ holiday pay and absence types. Among other things, the program integrates with Microsoft Office, Sage Payments, and Sage 50cloud Accounts. This allows you to create a software ecosystem that seamlessly connects to establish a strong business. Sage 50cloud Payroll is accessible via mobile and tablet devices. Papers and information, such as pay stubs, are available to you and your employees from any location.

Sage 50cloud Payroll is available in two versions: standard and professional. The standard edition costs £19.50 per month for up to 15 employees, while the professional plan costs $66 per month for up to 50.

8. Wave

Wave is ideal for small businesses with fewer than 10 employees, as well as self-employed individuals such as freelancers and consultants. This free payroll software is simple to set up and use, with a dashboard that contains all of the information you require.

Wave streamlines accounting and invoicing operations, allowing you to focus on growing your business rather than tracking spending, payments, personnel, and taxes. You can quickly create and submit professional invoices, estimates, and receipts, as well as assign these to recurring tasks. Furthermore, you can track them to keep track of your processes.

This software also allows you to scan receipts, connect to banks, and eliminate manual data entry, allowing you to speed up your process without sacrificing accuracy. You will also have the opportunity to prepare for tax season. Because the app is cloud-based, you can pay your team from anywhere by using online pay stubs or direct deposits.

As mentioned earlier, Wave is free with no hidden fees. Furthermore, it integrates with other apps such as PayPal, Etsy, Shoeboxed, Zapier, and Google Sheets, making your operation run smoothly.

9. Patriot Software

Patriot Software‘s Basic Payroll package allows small businesses to run payroll in three simple steps, but they must handle payroll tax deposits and filings themselves. Employers who do not have the time or resources to handle payroll tax deposits and filings should consider Full-Service Payroll, which includes all payroll tax filings for the year. Both packages include a web-based user interface.

Patriot Software offers unlimited payrolls with direct deposit and checks 24 hours a day, seven days a week. If you have one or more employees, you can use its scalable pricing approach to process their wages, giving you a lot of payroll expense flexibility and consistency. The software also supports a variety of payment schedules and provides W-2 templates. You also get a free employee portal where employees can access their pay data, as well as automatic tax updates for accurate wage calculations.

The basic package includes setup and US-based support, as well as a non-technical onboarding wizard. Meanwhile, by combining Patriot Software’s time and attendance and HR software, a complete HR and payroll suite is available. Nonetheless, it is compatible with Plaid for and QuickBooks.

For $10 per month plus, $4 per employee, small businesses can begin with the basic plan. Meanwhile, if you want Patriot Software to handle your tax filing as well, Full Service Payroll starts at $30 per month.

10. Zoho Payroll

Zoho Payroll is available in India as a standalone application and in parts of the United States, as part of Zoho Books. This web application is designed to automate and improve payroll operations by allowing you to consolidate employee records, as well as schedule and pay employees. In a nutshell, it can quickly calculate payroll, organize pay schedules, and execute and approve pay runs.

In addition to creating tax-ready reports, correct tax deductions, and automatic employee income tax returns with Zoho Payroll, you can also get solutions for employee onboarding, allowing you to simply add new recruits to your payroll and manage their information centrally. Your employees will also have access to a secure self-service site where they will be able to check announcements, files, and payroll information from a central location where payroll personnel and employees can collaborate.

Zoho Payroll can help you stay compliant by reminding you of tax payment deadlines and preparing necessary tax reports, returns, and filings. You can control who can administer or process payroll using role-based access. The administration, auditing, and financial teams can communicate easily while maintaining data integrity.

Zoho Payroll integrates with the Zoho family’s HR and accounting applications, Zoho People and Zoho Books. You can also begin with a free month-long trial, and if you find it suitable for your operation, you can begin with a plan at ₹50 per employee per month.

11. Zenefits

Zenefits is designed to help SMBs with payroll, benefits, and other employee-related tasks. It comes with tools for employee directory management, employee benefits, and insurance, recruitment and onboarding, ACA compliance, mobile support, and more. All these features and capabilities are consolidated into one dashboard for greater control, regulatory compliance, and employee information access.

This app makes online employee insurance management simple, allowing you to preserve your current plans or choose from a wide range of new benefits choices, while also helping you to stay compliant with the Affordable Care Act, by reporting employee benefit eligibility and coverages, and electronically submitting taxes to the IRS.

On top of HR solutions like onboarding, hiring, and record-keeping, Zenefits allows for automatic updates of payroll whenever changes are made to details on the platform. You also get deeper visibility into PTO utilization throughout your entire firm for better efficiency and management. Zenefits start at $45 per month.

12. Push

Push is an HR solution designed for companies in the retail, food and beverage, manufacturing, and construction industries. It combines software solutions for time tracking, staff scheduling, recruitment and onboarding, payroll, and reporting into a single platform.

Its facial recognition and geofencing technology, which tracks employee clock-in behavior and prevents buddy punching, is a unique feature of its time tracking capability. Employees can use a tablet or smartphone to clock in and out and set up automated time tracking rules. You also get centralized access to employee data and paperwork, such as hiring and onboarding information, employee performance, health insurance, certifications, and license renewals.

Push is a simple and inexpensive tool that can be used on any device that has an internet connection. It integrates with a variety of third-party apps, and you can test it out before committing to a package, which starts at $5 per employee per month.

13. ThePayStubs

ThePayStubs enables the quick creation of an electronic pay stub that can be used for proof of income, tax disputes, and other purposes. These paystubs are emailed to the recipient in the form of a print-ready PDF that can also be downloaded.

To generate a pay stub, simply enter all required information into the web form, such as state of residence, employee details, deductions, and check numbers. You can preview the stub while filling out the form. You can also choose a template that fits your requirements, place your order, and pay. You will receive the e-Stub via email once you have paid. You can do all of these in less than two minutes, no matter where you are.

PayStub Generator offers live customer support 24 hours a day, seven days a week, which is especially helpful to those who are unfamiliar with filling out pay stub forms or with tax season in general. The customer service team will walk you through the process and explain all of the jargon and statistics that may be confusing.

14. Justworks

Justworks assists managers and HR executives in keeping teams together and effectively managing needs. It provides payroll services and automation for businesses of different sizes, covering employee benefits, pay, leave, and other related issues.

Justworks pays all employees, full-time or part-time, on time and correctly. You can also use the software’s payment options and payroll capabilities, such as direct deposits, bonus and reimbursement administration, analytics, and reporting, to manage payments from clients, vendors, and suppliers. You can also establish employee or work policies such as leave, time off, vacations, and holidays. The digitization process aids in the improvement of precision and efficiency.

Finally, your employees receive their own individual dashboards, which include their profile, performance, and other vital information. This interactive portal allows them to view pay details, request time off, participate in company programs, and more. Pricing starts at $49 per month per employee.

15. Paylocity

Paylocity is a payroll and HR service aimed at the lower end of the SMB market. It offers self-service capabilities as well as seamless integration with leading retirement, general ledger, and time and attendance software. Its web payroll service assists you in reporting, compliance, pre-process registration, among other processes.

Paylocity, in addition to payroll processing, provides HR tools such as employee tracking, training, scheduling, and onboarding. However, this software is intended to do more than just simplify and streamline important payroll and HR processes. It also has a communication component that allows employees and managers to exchange notes. Performance evaluations have also been simplified. Furthermore, the insights and statistics assist you in making better decisions.

Paylocity can integrate with VOYA Financial, Principal Financial Group, Guardian, Cornerstone On Demand, and Empower Retirement. Meanwhile, the monthly fee for the package begins at $2 per employee.

Choosing Payroll Software for Startups

Starting a business is difficult enough without having to worry about payroll. Startups must address a plethora of business activities before they can perform consistently and make their names known. They will be able to do so more efficiently if they can automate one of the most time-consuming tasks in business—payroll. However, choosing the best payroll software for your startup may be tedious since many software packages provide much more than just payroll management, but do you really need all of those features?

In addition, it is best to formulate questions that are specific to your needs, such as whether you need a system that integrates with so many third-party apps, or whether you simply need something that works with the apps you currently use. Consider how the payroll software features benefit you rather than how many the software provides. In this way, you get more value for your money.

Key Insights

• Time Savings: Almost a quarter of small businesses spend four or more hours per week on payroll tasks. Payroll software can automate these tasks, freeing up valuable time for other critical business activities.
• Compliance Management: Only 36% of businesses are familiar with FICA regulations, which can lead to noncompliance issues. Payroll software helps ensure compliance with government regulations, reducing the risk of costly penalties.
• Employee Retention: Payroll errors can significantly impact employee satisfaction, with 49% of workers seeking new jobs after two payroll errors. Accurate payroll software minimizes errors, contributing to better employee retention.
• Cost Efficiency: Payroll software offers various pricing plans and features, making it accessible for startups with different budget constraints. Solutions range from free basic versions to comprehensive packages with advanced functionalities.
• Integration Capabilities: Many payroll software options integrate with other business tools such as accounting software, HR systems, and time-tracking applications, creating a seamless workflow and improving overall business efficiency.

FAQ

1. What are the benefits of using payroll software for startups?
   Payroll software automates the payroll process, saving time and reducing errors. It ensures compliance with tax regulations, improves employee satisfaction by providing accurate and timely payments, and integrates with other business tools for streamlined operations.
2. How does payroll software ensure compliance with tax regulations?
   Payroll software automatically calculates tax deductions, generates necessary tax documents, and submits filings to government agencies. It also provides reminders for tax deadlines and helps businesses stay updated with changes in tax laws.
3. Can payroll software handle different types of employees and payment schedules?
   Yes, payroll software can manage various types of employees, including full-time, part-time, and contract workers. It supports different payment schedules such as weekly, bi-weekly, and monthly, and allows for direct deposits and check payments.
4. What features should I look for in payroll software for my startup?
   Key features to consider include automated tax calculations and filings, direct deposit options, integration with accounting and HR software, employee self-service portals, and compliance management tools. Scalability and user-friendly interfaces are also important.
5. Is payroll software cost-effective for small businesses and startups?
   Payroll software can be very cost-effective, as it reduces the time and resources spent on manual payroll processing. Many software providers offer affordable pricing plans tailored to small businesses, ensuring that startups can find solutions that fit their budget.
6. How can payroll software improve employee satisfaction and retention?
   Accurate and timely payroll processing ensures that employees are paid correctly and on time, which is crucial for employee satisfaction. Features like self-service portals allow employees to access their pay stubs and tax documents easily, enhancing transparency and trust.
7. Do I need technical expertise to use payroll software?
   Most payroll software is designed to be user-friendly and does not require technical expertise. Many providers offer customer support and onboarding assistance to help businesses get started and make the most of their software.
8. What should I do if I encounter issues with my payroll software?
   Choose payroll software that offers robust customer support, including phone, chat, and email options. Check for software providers that offer comprehensive help resources such as FAQs, tutorials, and user guides to troubleshoot common issues.
9. Can payroll software scale with my business as it grows?
   Yes, many payroll software solutions are scalable and offer different pricing plans and features to accommodate the growing needs of your business. Ensure that the software you choose can handle an increasing number of employees and more complex payroll requirements.
10. How do I choose the best payroll software for my startup?
    Consider your specific business needs, such as the number of employees, payroll complexity, and integration requirements. Evaluate different software options based on features, pricing, user reviews, and customer support. Utilize free trials and demos to test the software before making a decision.

By Louie Andre

B2B & SaaS market analyst and senior writer for FinancesOnline. He is most interested in project management solutions, believing all businesses are a work in progress. From pitch deck to exit strategy, he is no stranger to project business hiccups and essentials. He has been involved in a few internet startups including a digital route planner for a triple A affiliate. His advice to vendors and users alike? "Think of benefits, not features."