Best payroll services for startups

Payroll services are essential for startups, managing time-consuming tasks like payroll runs, tax filings, and multi-state compliance. However, their capabilities can vary significantly, making it important to do your due diligence before hiring one.

Let’s explore five of the best payroll services to consider in 2025, including a mix of basic payroll providers and professional employer organizations (PEOs), to help you find the best payroll company for your business.

5 best payroll services for startups: Pros & cons

1. Zeni Payroll 

Zeni is a comprehensive financial management platform. In addition to our AI-powered bookkeeping, tax, and fractional CFO services, we offer expert payroll management and support.

That includes employee onboarding and termination, payroll system set up and management, and compliance assurance across all states and jurisdictions. We also offer the option to customize your subscription with various add-ons, ensuring you only pay for what you need.

Pros:

• Integrates seamlessly with our full suite of financial products and services, including our employee reimbursement and bill payment software, both of which come free with every bookkeeping subscription
• Leverages AI-enhanced workflows to improve accuracy and reduce the need for manual work
• Capable of managing compensation for full-time employees and independent contractors. Includes international contractors as an add-on, making Zeni a scalable payroll solution no matter how big your team grows or where they work
• Highly customizable through payroll add-ons, including state registrations, W-2 and 1099 filing, benefits administration, and state account closures

Cons:

• Payroll services can be purchased individually, but Zeni is best suited for startups seeking an integrated financial management solution that handles everything in one place
• Monthly subscriptions may be more expensive than less comprehensive payroll services

2. Gusto Payroll

Calling itself “The People Platform,” Gusto is a payroll provider that serves more than 100,000 U.S. businesses. In addition to managing payroll, Gusto’s automated platform has the capability to assist with employee benefits and HR tasks like time tracking, hiring, and onboarding. 

Pros

• The platform is easy to set up and offers a modern, intuitive, user-friendly interface, as well as easy payroll integration with other popular tools. At Zeni, about two-thirds of our customers are outsourcing payroll to Gusto.
• Companies of any size can use the platform—there is no minimum number of employees required, making it ideal for startups and small businesses' payroll. Conversely, PEOs require at least seven employees to sign on. 
• It is the lowest-priced startup payroll system in this comparison, beginning at just $19 per month for unlimited payroll runs.

Cons

• Gusto requires employers to handle registering their employees in multiple states, which can be a complicated process and puts the onus of ensuring your business is compliant with regulations on the employer. If you have employees working outside the state where your business operates, you’ll need to research and understand that state’s legislation and then carry out the necessary steps for proper registration.
• As strictly a payroll service provider, it does not offer shared liability for employment law compliance. 

3. Justworks

Justworks is a PEO.  It offers a Basic plan and a Plus plan; Basic pricing begins at $49/month for companies with 49 or fewer employees and decreases as the number of employees increases. Payroll-specific features include:

• Running payroll for salaried and hourly employees
• Off-cycle payments
• Vendor and independent contractor payments
• Filing employer payroll taxes
• W-2 and 1099 filings
• Unemployment insurance filings
• Employee self service
  
  

Pros 

• The platform makes it easy and affordable to pay contractors; clients don’t incur a per-employee cost. 
• Customer service is comprehensive and reliable; it earns high marks from users. 
• Compared to TriNet, it offers lower rates for insurance options in certain parts of the country. However, this decision comes down to your company’s census. We recommend our clients consider both options because their pricing structures are similar (though presented differently). 
• The platform is stable and intuitive; notifications and emails, in particular, are user-friendly. 

Cons

• As with other PEOs, Justworks is more expensive than a basic payroll company. If you only need a product to run payroll, a PEO may offer more than you need (and cost more). 

4. TriNet

TriNet is another PEO option we recommend for startups that want the PEO-specific features in addition to global payroll services. You can learn more about TriNet’s specific payroll services here. Depending on the location of your business, TriNet’s pricing may be the most competitive. Keep in mind that TriNet and Justworks offer similar benefits. Between these two reliable and feature-rich platforms, it boils down to comparing the price point for each platform.

Pros

• Like Justworks, TriNet’s customer service is comprehensive and reliable; users give it high marks. 
• The platform is reliable and easy to navigate. 

Cons

• TriNet charges extra to pay contractors, which could be a detriment for startups. At Zeni, if we have clients who partner with TriNet, we choose not to pay through TriNet so our clients don’t incur charges. 
• Despite a recent UX overhaul that modernized the platform, certain features like email notifications are still copy-heavy and may feel overwhelming. However, in our opinion, TriNet’s content is more accurate and clear than other payroll providers, even if TriNet doesn’t “feel” modern.

5. Rippling

Rippling is a newer contender in the space; you can view its payroll processing features here. Pricing starts at $8 per month per user. With its recently launched PEO, Rippling helps employers manage your employees' payroll, benefits, devices, apps, and more from one place.

Pros

• The platform is attractive and easy to set up. 
• It offers full-scale automated payroll processing in addition to PEO solutions.
• The platform’s unique combination of HR & IT features—things like automatically sending app invites to new employees during the onboarding process—are particularly appealing to startups. While there does appear to be some bugs in the system currently, we think Rippling may be one to watch for the future.

Cons

• Customer support is lacking.
• Problematic issues have plagued payroll systems and API management. 
• Although it feels modern and has a user-friendly look, Rippling falls short in terms of stability and may not be the best payroll automation option yet. 

How do you choose between a payroll service provider and a PEO

Aside from cost, consider the following factors to help you decide between a payroll service provider and a PEO:

• Do you have enough employees to support a PEO partnership? PEOs require a minimum number of employees. To make this decision, first assess how quickly you’re going to grow, and then think about where you’re going to grow. If you plan to hire employees in multiple states, a PEO is a wise idea.

• Do you need to offer benefits? PEOs provide benefits at scale for their clients’ employees; payroll providers do not. If competitive benefits are a consideration for your organization, you will be better off partnering with a PEO. 

• Do you only need payroll features? If so, a solution like Gusto is your best option. If you would like the full service payroll process offered by a PEO, compare features and costs before you make a decision. 

Payroll software solutions: A head-to-head comparison

…best payroll service

No matter which payroll provider you use, Zeni can help you manage them.  

Whether you choose to partner with a payroll service provider or a PEO, Zeni can help seamlessly orchestrate your payroll operations. With our Payroll Manager service, we coordinate payroll tasks between you and your online payroll solution: registration in various states; initial follow-up, advising, and sending reminders to employees to complete compliance forms; and preparing other required documents and banking information (like I-9s, W4s, pay stub samples, and more).

 Zeni is an all-in-one finance automation platform for startups that takes care of all your finance functions, from daily bookkeeping to taxes to real-time reporting to payroll data management. Our experienced team of accountants, tax advisors, and CFOs know the world of startup finance inside and out, so we’ve seen the challenges many founders and business owners face and can provide expert guidance for every scenario.

If Zeni sounds like the right fit for your business, get in touch with our team to learn more.

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