Managing payroll for a small (S) corporation comes with unique challenges that require careful attention to Internal Revenue Service (IRS) regulations, especially when it comes to compensating shareholder-employees correctly. Choosing the right payroll software can simplify this complex process by automating tax calculations, ensuring compliance, and streamlining employee payments.

Whether you’re a small S-corp just starting out or a growing business looking to scale, finding a well-suited payroll solution is essential for maintaining smooth operations and avoiding costly penalties. In this blog, we will explore the best payroll software for S-corp, helping you make an informed decision that saves time, reduces errors, and supports your business growth.

Top 7 Payroll Platforms For S-Corp

Comparison Table

Software

Our Ratings

Top Features

Free Trial

SurePayroll 

4.5 

★★★★★ 

Automated payroll 

Custom templates 

No 

OnPay Payroll  

4.7 

★★★★★ 

Custom onboarding workflows 

Workers' comp 

Yes  

ADP Workforce Now 

4.5 

★★★★★ 

Automated time monitoring 

Live HR support 

No  

Patriot Payroll  

5 

★★★★★ 

Free direct deposit 

Employee self-service portal 

Yes  

Gusto HR Software  

4.5 

★★★★★ 

Personalized reports 

Payroll support in 120+ countries 

No  

QuickBooks  

4.5 

★★★★★ 

Project tracking 

Custom invoices 

Yes  

Wave Payroll 

4.5 

★★★★★ 

W-2 and 1099 forms 

Unlimited bookkeeping records 

Yes  

1. SurePayroll

SurePayroll by Paychex is an online payroll software solution that optimizes payroll processing, HR tasks, tax management, etc., for small businesses, including S-corp. It automates payroll cycles, calculates and files taxes, and provides direct deposit services, all accessible from any smart device. By partnering up with Paychex Insurance Agency, the software helps employers find and employ the best healthcare plans for their workforce.

Top Features

  • Tax filing (local, state, and federal)
  • Free direct deposit
  • Custom templates for compliance
  • Automated payroll system

Pros And Cons

Pros
  • The software accurately runs payroll in just a few minutes
  • Offers an efficient breakdown of money taken out of each paycheck
  • Year-end tax forms help users stay compliant with the law
Cons
  • The reporting feature may be a bit unintuitive for some users
  • The auto-populated dates are not in order and users need to change them manually

Pricing

The software offers two pricing plans for small businesses: No Tax Filing ($20/month + $4/employee) and Full-Service ($29/month + $7/employee).

Disclaimer: The pricing is subject to change.

2. OnPay Payroll

OnPay Payroll is a full-service payroll software that optimizes payroll, HR, benefits management, etc. It helps users pay employees and contractors in just a few clicks and automatically handles all calculations, deductions, and payroll taxes to ensure accuracy and compliance. The software seamlessly integrates with accounting platforms and benefits providers, making it easy to keep everything in sync and reduce potential errors.

Top Features

  • Payroll automation
  • Custom payroll reports
  • Personalized onboarding workflows
  • Workers’ compensation

Pros And Cons

Pros
  • Efficient payroll functionality that helps pay employees on time
  • Employees can easily access and download their paystubs
  • In case of holidays, the system notifies users to run payroll early
Cons
  • The lack of a comprehensive reporting tool makes users print out multiple reports for effective data evaluation
  • W-2 forms cannot be personalized to different formats

Pricing

The platform costs a base fee of $49/month plus $6/employee/month. It also offers a 30-day free trial.

Disclaimer: The pricing is subject to change.

3. ADP Workforce Now

ADP Workforce Now utilizes its cloud-based technology to provide comprehensive payroll and HR solutions, trusted by businesses of all sizes. Designed to help organizations manage payroll efficiently, it offers automated payroll processing, tax filing, and compliance support—all in a centralized platform. S-corp owners can particularly benefit from its features that streamline employee payments, ensure accurate tax withholdings, and support regulatory compliance, which is crucial for managing shareholder-employee compensation.

Top Features

  • Automated time and attendance monitoring
  • Shift scheduling
  • Automated payroll processing
  • Live HR support

Pros And Cons

Pros
  • The software offers powerful HR tools to streamline diverse administrative tasks
  • Users can easily find and download paystubs within the system
  • It is a unified platform that houses all the essential information in one place
Cons
  • The reports cannot be customized to users’ needs
  • The management of electronic 1099s can be a bit difficult

Pricing

ADP Workforce Now offers custom pricing packages: Select, Plus, and Premium. All plans provide payroll, onboarding, and HR services. In addition, users can also get additional features for an extra fee.

4. Patriot Payroll

Patriot Payroll is a powerful accounting software that streamlines payroll, bookkeeping, and similar functions. Businesses can create, send, and monitor invoices while generating detailed financial reports to accurately manage and evaluate payment data. Plus, the software allows users to run unlimited payroll by utilizing its full-service payroll service. Moreover, Patriot helps organizations efficiently track the workforce’s time and attendance, sync its data with payroll, and run precise and error-free pay cycles.

Top Features

  • Unlimited payroll processing
  • Free direct deposit
  • Employee self-service portal
  • Custom HR documents’ templates

Pros And Cons

Pros
  • The software timely files state and federal taxes, ensuring users’ compliance
  • Efficient timecard application and administrators can easily approve them for processing
  • It seamlessly integrates with other accounting platforms, streamlining business operation
Cons
  • The reporting feature can be a bit cumbersome to use
  • The lack of an editing feature in paid time off (PTO) functionality can be a bit inconvenient

Pricing

The software offers two pricing plans: Accounting Software, which further offers two sub-plans (Accounting Basic at $20/month and Accounting Premium at $30/month), and Payroll Software with two sub-packages (Basic Payroll at $17/month + $4/worker and Full Service Payroll at $37/month + $5/worker).

Patriot Payroll also offers a 30-day free trial.

Disclaimer: The pricing is subject to change.

5. Gusto

Designed particularly for startups and small businesses, Gusto has built a reputation for its powerful payroll and HR services. It automatically files users’ taxes in all 50 U.S. states, ensuring their compliance and reducing workload. The platform also helps administrators get valuable insights from licensed advisors and create health insurance plans for their employees. Along with time monitoring, talent and performance management, and more, Gusto ensures S-corps can focus on their workforce and efficiently manage day-to-day administrative tasks.

Top Features

  • Auto-tax calculations
  • International payroll (120+ countries)
  • Custom reports
  • Employee pulse surveys

Pros And Cons

Pros
  • The mobile app allows employees to track and manage their paystubs, billable hours, and documents
  • Administrators can easily add new employees to the system and share essential information with them
  • The unified platform allows users to easily locate tax documents and work on them, whenever needed
Cons
  • Some features that can be edited and personalized on the mobile app cannot be edited on the web version, and vice versa
  • The lack of in-app reminders for timesheets may result in missed clock-ins on busy days

Pricing

The platform offers three pricing plans: Simple ($49/month + $6/month/person), Plus ($80/month + $12/month/person), and Premium ($180/month + $22/month/person).

Disclaimer: The pricing is subject to change.

6. QuickBooks Intuit

The platform assists accountants and small organizations in efficiently managing payroll management, invoices, and tracking labor costs. By utilizing its cloud-based accounting services, businesses can easily store and migrate data between different platforms and make informed accounting decisions. QuickBooks Intuit provides a 360-degree view of sales and personalized reports, helping employers efficiently evaluate financial matters and do what’s right for their business.

Top Features

  • Personalized invoices
  • Inventory management
  • Data migration
  • Project tracking

Pros And Cons

Pros
  • Administrators can delegate critical accounts’ access to accountants, allowing them to easily log in
  • Employees can access their financial data, check their transactions, and view their remaining balance
  • The software seamlessly integrates with several third-party platforms and makes business processes easier
Cons
  • The mobile app poses some restrictions that the web version does not, such as the creation of custom reports
  • The software provides limited template options for reporting and documents

Pricing

In addition to a 30-day free trial, the software offers four pricing plans: Simple Start ($35/month), Essentials ($65/month), Plus ($99/month), and Advanced ($235/month).

Disclaimer: The pricing is subject to change.

7. Wave Payroll

Wave Payroll helps organizations manage and track transactions, create personalized invoices, and streamline accounting tasks. S-corp with a limited budget can effortlessly run payroll, pay employees and contractors on time, and maintain tax compliance. The software helps users avoid legal trouble at all steps and supports online payments via several channels, including credit cards, Apple Pay, and bank deposits.

Top Features

  • Automatic payments
  • 1099 and W-2 tax forms
  • Unlimited bookkeeping records
  • Automated bank transactions

Pros And Cons

Pros
  • Comprehensive payroll functionality that helps track and manage expenses and invoices
  • The software offers integration of automation that streamlines receipt scanning and payment transactions.
  • It allows users to instantly transfer payments to employees and contractors
Cons
  • The reporting functionality offers limited customization options
  • The software’s lack of integration with the transportation industry can impact some businesses’ operational

Pricing

Wave offers a free Starter Plan and a Pro Plan ($16/month). For receipt management, a dedicated Receipts plan is available (at $8/month), although this feature is also included in the Pro Plan (at $16/month).

Additionally, professional Bookkeeping support (from $149/month) and Accounting coaching (from $229/month) are available as optional services.

Disclaimer: The pricing is subject to change.

Choosing The Right Payroll Software For S-Corp

Winding up the above discussion, all the above-mentioned platforms help small businesses and S-corps effortlessly manage financial data and make analytical decisions. However, choosing one platform can be a bit challenging and requires considering several factors, including your workforce size, budget bracket, immediate requirements, etc.

That said, if you are looking for a software that helps you manage payroll as well as workforce tasks, Gusto should be your go-to platform. Patriot Payroll and QuickBooks Intuit are ideal for users needing comprehensive payroll and accounting services. Similarly, for firms needing invoicing and financial management platforms, Wave Payroll can serve them best.

If you are still confused about the right choice and need an expert opinion, get in touch with our software experts and they will help you make a cost-effective decision.