8 Best Payroll Software for Startups

Best Payroll Software for Startups

To have a simplified financial system, optimizing your payroll processing can be crucial. This allows you to avoid paying a large payroll tax penalty, and it keeps your employees happy.

High-quality payroll software is the best way to manage your payroll process. This article will highlight the top 8 solutions.

8 Best Startup Payroll Software

These are the top 8 payroll platforms that will optimize your payroll management.

1. FreshBooks

When running payroll, mistakes can be made by manually entering data and tax filing. FreshBooks is available so you don’t need to risk it.

The user-friendly payroll software was originally developed to manage invoices. It has evolved to be one of the most comprehensive accounting products available. It’s now used in over 150 countries.

FreshBooks does not have payroll processing built in. It seamlessly integrates with Gusto, a well-known platform. FreshBooks offers 4 plans. You can choose from any one of them after a free month-long trial. Your company’s complexity and size will determine which plan is best for you.

If you have large amounts of payroll data and multiple tax filings, the Premium or Select plans might be a good option. To learn how to manage employee bank accounts, you can also use webinars.

  • Unlimited pay runs
  • Direct deposits
  • Automated tax filing and payment
  • 1099s and W-2s
  • Automatic payroll transactions pulled into different accounts

This platform is ideal for filing taxes. The platform calculates how much you must pay and automatically files them with the appropriate agency. This will help to avoid costly mistakes.


  • Use it quickly
  • Large selection of plans
  • Automated filing of federal, state, and local taxes
  • Time tracking features
  • Automated bank account transactions
  • Excellent customer support


  • Integration with Gusto is required

Also read: 10 Best Invoicing Software for Small Businesses

2. Gusto

Gusto is a startup-friendly payroll program. It offers several features that will help you keep track of workers’ compensation.

It doesn’t charge tax services in many states, unlike other payroll companies. Startups will find this important because it eliminates the need for them to pay payroll taxes.

The full-service payroll system also includes an onboarding process. You will need to provide basic information about your company and you’ll be sent an email informing you how to complete the rest. You can also downgrade or upgrade your plan at any time.

Gusto’s high-quality administration of health benefits is another attractive feature. You can have workers’ compensation and health insurance managed by Gusto. It can also help you sign up your employees for different benefits plans.

Gusto is a great platform but it’s not perfect. Gusto’s biggest problem is its customer support. It is available only from 7 A.M. until 4 P.M.


  • Multiple regions get simplified state payroll taxes
  • Interface for beginners
  • Small businesses can save money
  • A great way to manage employee benefits


  • Limited customer support is available

3. QuickBooks Payroll

The most difficult part of using software for your payroll service is the onboarding process. QuickBooks makes this process easy.

You don’t need to be an expert in payroll programs to create an account. With QuickBooks, payroll setup is easy. You can access your “Payroll” menu to do the majority of the work.

For assistance, you can also contact their technical support between 6 A.M. – 6 P.M.

QuickBooks offers a variety of advanced and basic payroll features. They are organized into columns by the platform.

  • Employer
  • Regular pay hours
  • Method of payment
  • Memo
  • Total pay
  • Hours worked by total employees
  • Overtime
  • Bonus

There are some drawbacks to QuickBooks. It doesn’t always update data at the right time. This makes it more vulnerable to losing tax withholding information and other important data. The platform is also susceptible to system crashes.


  • The best payroll software available for new users
  • Support available for customers
  • There are many features


  • The frequency of updates is questionable
  • Recurring crashes

4. Rippling

Rippling is a highly-rated HR software, that has many quality payroll features. You can run payroll faster and more efficiently with Rippling, as it handles all aspects of HR.

For example, The “Time Off” feature is extremely useful. This allows you to see your employees’ vacation hours. It is easy to use and allows you to calculate vacation pay in seconds.

Your workers can request time off without ever having to use payroll platforms. Each request is sent to you via email, which allows you to view them before submitting them. You can then spend more time on money-making activities and less on administrative tasks.

Other features can also be accessed easily. With just a few clicks, you can access important payroll and employee information.

Rippling’s biggest problem is its lack of core features for the smartphone version. Rippling might not allow you to access the “Insurance and Benefits” section of your Android device.

Android users may not be able to access certain tax forms. They might only be available in the browser version.


  • Outstanding HR tools to ensure smoother payroll processes
  • Important “Time-off” feature
  • Documents that can be easily retrieved


  • Poor customer service on smartphones
  • You could be prevented from paying taxes on time by not having the correct tax information


TriNet offers many features that will help startups improve their payroll management.

Remote teams can be used to support your business. You shouldn’t have any problems managing your insurance and benefits. It keeps up-to-date with all state laws in order to ensure compliance. You will also be familiarized with federal taxes in order to reduce the chance of being fined.

The intuitive interface is also appreciated by users. The menu navigation is easy, so it doesn’t require tech-savvy for your team to use the platform.

TriNet makes it easy to manage your HR tasks. It offers access to capital expertise and risk mitigation as well as many other insights.

TriNet is expensive, so it’s not affordable for many startups. Processing 1099s requires additional fees.


  • This guide will help you to understand the tax laws
  • Convenient interface
  • Helpful HR advice


  • The price is high

6. Zenefits

Zenefits is similar to Rippling. Most of its features promote easier HR management. Third-party apps can provide payroll functions as an additional feature.

The payroll section can be accessed from the homepage. You will find many useful features such as:

  • Timely pay employees
  • Comprehensive payroll overview
  • Visit your Timeline (administrative modifications)
  • Setting up reports and settings

The platform is available to startup owners, but it takes a more advanced approach to benefits and HR. The starting price for one employee is high, and it can be difficult to learn navigation tools. It might be more beneficial for larger organizations.


  • This tool will help you keep on top of your HR responsibilities
  • Payroll software add-on is easily accessible
  • Solid payroll management features


  • Established companies might be better suited

Also read: What is Payroll Outsourcing? Benefits, Practices, And Work

7. Wave Payroll

Wave Payroll lets you manage taxes, employee deductions, and payroll from one location. This full-service payroll provider allows you to run payroll for employees and contractors.

Wave Accounting can also be connected to the app by your team. The platform can also file your payroll taxes in certain states. Your employees will also have access to their personal information via a portal.

These are the states in which Wave Payroll calculates, pays and files payroll taxes automatically:

  • Florida
  • Arizona
  • California
  • Illinois
  • Georgia
  • New York
  • Texas

If your company is located in one of these states, you will be protected from tax penalties.

Wave Payroll can automate all tax forms, including W-2s and 1099s. Wave Payroll supports direct deposit payments, and you can manage deductions.

It does not have some of the features that you will find on other platforms. It doesn’t let you manage or buy benefits plans. It does not provide tools that can help with garnishment management.


  • Many states allow tax filing
  • Contractors and employees can work together
  • Wave Accounting allows your employees to connect to Wave Accounting
  • Direct Deposit Payments and Deduction Management


  • Lacks garnishment management

8. SurePayroll

SurePayroll is the last payroll app on our top-rated list. The app offers excellent documentation and tax assistance. It also offers reliable customer support.

The Full-Service plan also allows unlimited payroll runs. It also calculates, pays, and files taxes.

SurePayroll’s strength is its affordability. It is much more affordable than other full-service payroll providers.

SurePayroll’s biggest problem is its inability to work on smartphones. While it’s optimized to work on desktop computers, bugs plague both the Android and iPhone versions.


  • Unlimited payrolls
  • Total tax management
  • Good customer support


  • Smartphone configuration could be improved

Key Takeaways — Best Payroll Software for Startups

These 8 payroll services are unbeatable. FreshBooks may be the best choice. You can customize your payment schedules and file taxes right on time thanks to its integration with Gusto. These services are vital for professional employer organizations.

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