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10 Best Payroll Software Solutions for Small Business in 2020

Over the past ten years, cloud technology has transformed the payroll software. Therefore, companies and individuals no longer spend time on the most time-consuming payroll tasks like time cards, printing checks, or combining through time cards for individual changes over the time period.

Payroll software enables you to calculate wages, pay employees through direct deposit and file taxes. Making sure you pay the employee in full and on time is a key factor for a high functioning team, which makes a choosing payroll software for small business a crucial decision.

Plus, payroll professionals ensure that direct deposits send correctly, watch for exception and edge cases, and manage the automated process.

Payroll processing envelops computing employees’ gross pay, withholdings, net pay, printing payroll checks, preparing payrolls for management, and preparing payroll tax returns.

Types of Payroll Software

Payroll software needs to be chosen toward company size since, there’s no one size fits it all solution. Some vendors may offer solutions available just for small businesses or large enterprises, while others provide a range of solutions designed for specific company types.

If you’re planning to use payroll software for your business, these are the best solutions:

  • Made for small business (less than 50 employees);
  • Designed for medium-sized business (50 to 100 employees);
  • Recommended for larger companies (100+ employees, multiple locations, locations in different countries, etc.).

Payroll Software Features

Most payroll software offers main features such as tax management, printing checks/direct deposits, payroll processing, and more.

Still, depending on the software, some features may be standard, while others may be add-ons or not offered at all.

Bellow, is the list with the most common features of payroll software:

1. Payroll processing – With adequate software, processing payroll can be performed in relatively no time. Most solutions have integration capability, which, depending on your platforms for payroll and timekeeping, can link systems together to pull hours automatically, process payroll, pay rates, print checks, and make ACH (automated clearing house) deposits.

2. Time & attendance management – This feature records the employees working time. Employees can clock in through this system or by a manual time clock system. Salaried employees can fill either a manual or an electronic time sheet. This feature also monitors of vacations and sick time. Some payroll systems have the time & attendance feature built in, but others may need integration with an attendance module.

3. Tax management – The tax management automatically calculates the federal, state, local, and other social security-medical care taxes that are deducted from each employee’s paycheck. It also automatically updates any tax code changes and alerts the user.

4. Benefits management – Benefits management can either be a separate module or a built-in feature, depending on the software. Employees can keep track of benefits offered, such as insurance, retirement, vacation/sick, and other benefits.

5. Reporting – Best small business payroll software solutions deliver reporting features such as gross-to-net payroll register, tax reports, deduction analysis, compensation analysis, and more. Reporting templates are typically offered. Plus, you can create custom reports.

6. Integration – Majority payroll software can integrate with another system, such as HRMS (human resource management system) or accounting software. You may also have separate modules for benefits and time & attendance that can integrate with payroll solutions.

7. Mobile functionality – It’s another feature that’s becoming more common in payroll systems. Not only can employees see their paycheck on their mobile device, but they can also launch payroll form their tablets or smartphones.

8. Direct deposit – With direct deposit, you save thousands of dollars annually in processing costs and supplies, employees no longer have to worry about check fraud or lost checks. Plus, funds are transferred from company accounts directly to employees through ACH and are available instantly unlike traditional checks that typically have a holding period.

Best Payroll Software Systems in 2020

Whether you’re seeking for a free payroll software or you’re willing to pay for full-service payroll software, there are some great solutions out there for you. Therefore, pay attention to these 10-best payroll software systems on the market right now.

Patriot Software Payroll – Best Payroll Software for Small Business

Patriot Payroll is an integrated HR (human resource) and payroll management system that streamlines the various processes linked with managing payroll payments and tax submissions.

This solution provides tools to maintain payroll records, print checks, establish direct deposits into bank accounts, generate payroll reports, and submit federal and state taxes.

Patriot Payroll can also issue payrolls through direct bank deposits and electronic cheques. The software has personalized portals for employees to access their financial and payroll information. The app’s reporting functionality enables employees to generate their year-end reports and print W2 forms for tax reporting.

While Patriot Payroll is an independent payroll system, the solution can also integrate with other Patriot Software solutions such as Patriot HR (personnel tracking) and Patriot TIME (time and attendance) to provide a full-fledged HRM suite.

For $7.50 a month, you'll get a non-accountant friendly finance management suite, and track cashflow like a professional.

QuickBooks Pro

QuickBooks Pro is a great accounting solution designed for small and midsize customers. The solution includes robust functionalities of a core accounting software application, such as project accounting, account payable and receivable, payroll management and expense management, all in one integrated suite.

With a Bank Account Reconciliation feature, users can link their bank accounts and define workflows for the accounting operations. It enables you to make automated payments and deposits from a linked bank account and also manage the employee payrolls by the app.

This QuickBooks payroll software solution also automates the invoicing and billing process and run order management from a single reconciliation window.

You can sync, link and import data from other integrated apps, such as American Express, Square, and PayPal. All transactions are automatically categorized to record monthly earnings and expenses.

QuickBooks Pro offers self-service payroll for $17.50 and full-service payroll for $40.


Gusto is a fully featured payroll, benefits administration, and compliance management platform. Designed to catered mainly small business across the States, Gusto has tools to manage core HR needs such as hiring, onboarding, time tracking, and training.

With a dedicated online account, an employee can fill out its personal info into the system and monitor all paperwork at one central place. Business can automate their payroll activities by scheduling payment and benefits release.

Payments can be issued by check or through direct bank deposit. The solution automatically brings electronic payslip to employee’s inbox upon completing the transaction.

This solution automatically calculates, pays, and files a company’s federal, state, and local payroll taxes.

Some of the extra features include custom reporting, multiple pay rates, multiple pay schedules, and third-party calendar integrations.

Gusto offers three pricing plans + 30-day free trial.

  • Core - $39/month + $6/month per person;
  • Complete - $39/month + $12/month per person;
  • Concierge - $149/month + $12/month per person.


RUN launched by ADP, is a web-based payroll system made for small businesses. The solution can be deployed on iPads, iPhones, or any other touchscreen device. RUN can integrate with multiple third-accounting software and human resource management service from ADP.

RUN provides cash flow management by letting users track and verify cash requirements before processing the actual payouts. With built-in reporting and analytics features, users can supervise and see a complete analysis of their monthly payroll activities.

This system also has a dedicated HR portal to save all critical info at one place with online storage for employee documents. HR411, the online resource form ADP, provides day-to-day practices for businesses.

Paychex Flex

Paychex Flex is a modular, web-based HCM (human capital management) solution designed to meet the needs of employers of any size and industry. With a single login, you can access recruiting and ATS (applicant tracking system), onboarding, human resource information system (HRIS), benefits administration, payroll retirement, time and attendance, and more.

Made on a central platform, applying a single data profile for each employee, Paychex Flex traces information in real-time and via the customizable apps.

Some of the essential software features include applicant screening, electronic onboarding, job/labor costing, garnishment payments, drag-and-drop visual scheduling, and automatic compliance testing.

Paychex offers multi-tiered solutions for customer service (CRM), which lets companies select from various options to fit their size and complexity best.

The Paychex app is free and allows employers and employees to access information such as tax documents, employee profiles, and check stubs.


Zenefits is a cloud-based HRIS that features user dashboards, core human resources, benefits administration, onboarding, and employee scheduling.

When new employees are hired, human resources professionals using Zenefits only need to complete 5 online fields to begin the onboarding operation. Employees sign all agreements online, and Zenefits can automatically process their info.

When employees leave, HR can remove them from payroll and benefits while initiating COBRA (consolidated omnibus budget reconciliation act) setup with a single process. Zenefits also provides an employee service portal.

It can integrate with payroll, health insurance, and other systems, and you can also set up new payroll, insurance, retirement plans and more. This solution has a development team that makes weekly changes based on user feedback.

Zenefits includes payroll software free, standard package ( $5/employee by month plus $40 base fee by month), and advanced package ($9/employee by month plus $40 base fee by month).


Xero is a web-based small business payroll software. Xero associates small businesses with their trusted advisors and caters business owners with instant visibility of their financial position.

As a web based-system, Xero can be accessed from any device with the Internet connection. With Xero’s excellent accounting features, small companies can monitor their cash flows, transactions, and account details from any location.

Bank transactions are automatically imported and coded. Online bill pay keeps track of spending and stays on top of bills due, upgrading relationships with the vendors that deliver critical business materials.

With Xero, personal expenses can also be maintained with mobile review and approval of each receipt. Xero has unlimited user support and integration with a variety of systems. This system comes with a 30-days free trial period for product testing and feature evaluation.

Prices vary by region/country, but in the States, subscription rates start at $9 per month.


OnPay is cloud-based payroll solution that helps small businesses automate tax filing and payment workflows. Key features include automated payroll taxations, new hire reporting, scheduled pay runs, and employee self-onboarding.

OnPay provides an employee portal for updating information, tax forms, and accessing past pay stubs. Businesses can track their employees’ paid time off (PTO), sick leaves, and vacation. The solution provides a document vault for storing employee notes and contacts.

It enables integration with third-party applications like QuickBooks, Xero, Humanity, Kabbage, Guideline, and more.

Great employee management feature powered by OnPay is 401 (k) planning for retirement. The solution operates compliance, deductions, and investment portfolios for users. It also allows employees to access their W2 forms and pay stubs online.

The base fee is $36 per month and users (employers and employees) can be added for $4/month by the user.


UltiPro is a cloud-oriented HCM (human capital management) system designed to help organizations manage their HR, payroll, and talent needs.

A configurable solution, UltiPro has functionality for recruiting/onboarding new hires, calculating/processing payroll, managing time/labor, developing employees through performance, administering workplace surveys, compensation management, and more.

Companies can also leverage UltiPro’s suite of embedded predictive and prescriptive analytics tools, as well as UltiPro’s business intelligence and report, across all of its solutions.

UltiPro offers employees role-based access for completing such task as managing pay and benefits information, setting and tracking goals, and requesting time off.


Namely is a cloud-based solution for companies searching a single comprehensive system to manage their human capital. Namely assists small companies to manage compliance and streamline everything -payroll, benefits, and talent management.

Namely is a fit for companies in just about any industry and is appropriate for businesses looking for a platform that can be configured to meet their unique company infrastructure.

Plus, Namely's HRIS provides a centralized location to store employee information. It offers an employee database with time off, reporting, and a social news feed.

Namely’s payroll module also handles payroll taxes, 1099s, W-2s, and ACA (affordable care act) reports. Integrated benefits administration helps with enrollment, and it automatically sends elections to carriers.

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