The Best Payroll Software for Small Business in 2024


best payroll software for small business

If you are searching for the best payroll software for small businesses in 2024, this article will guide you in the right direction by helping you save time, money, and effort in the long run.

Being a responsible small business owner, you must pay your employees accurately and on time. You should also file and remit payroll taxes accurately to the IRS without any delay.

Having in-house payroll software will help you administer payroll with total control, and save you time, money, and costly mistakes.

MUST-READ: How to do Payroll for a Small Business – The Ultimate Guide

The following are some of the reasons why the best payroll software will speed up your payroll process, and ensure accuracy and compliance with the IRS mandate.

  • Automatic calculation of federal and state taxes
  • Calculation of deductions and employee benefits
  • Handling payrolls across multiple states
  • Generation of payslips
  • Calculation and filing of employment taxes
  • Compliance with the IRS regulations
  • Management of time off, vacations, and sick leaves
  • Tracking employee time
  • Payment processing for the employees
  • Depositing payment via direct deposit
  • Printing of checks
  • Generation of payroll reports
  • Handles W-2s as well as other yearend reporting
  • Generation of general ledger report
  • Integration with popular accounting solutions, time-tracking solutions, and ERP systems

Before we start, you should understand that payroll is one of the most important components of your business, and in this article, we’ll cover the best payroll software for small businesses – CheckMark Payroll Software. We’ll go over the features, benefits, and setup process that will help you determine whether it suits your business or not?

Best Payroll Software for Small Businesses: CheckMark Payroll Software

CheckMark Payroll Software will make your life easier.

CheckMark offers a complete array of payroll features for your small business – from basic payroll needs to a full-service payroll including online payroll, time and attendance, direct deposit, tax filing, and payroll benefits administration, just to name a few.

One of the most useful and cost-saving features is the ability to add unlimited companies & employees and run unlimited payrolls.

If you have multiple stores or business locations, you don’t have to purchase multiple licenses. In one license you will be able to add all your stores, and employees and run payroll with great convenience.

As a small business owner, you know how the expenses rise day by day. With CheckMark Payroll Software at your side, you can rest assured that you can process payroll for one or a thousand employees for the same cost. This benefit allows you to have total control over the payroll cost.

Setting up CheckMark Payroll Software is straightforward. It automatically calculates federal tax, Social Security Tax, Medicare Tax, Unemployment Tax, 50 state taxes, local taxes, and much more.

You can also define incomes & deductions for nearly every need. Some of the pre-loaded incomes are – Advance, Allocated Tips, Bonus, Commission, Fringe Benefits, HSA-Co, Ins Benefit, Life Ins > 50K, Jury Duty, Lodging, Mileage, Piecework, Profit Share, Reimburse, Reported Tips, Retro Pay, Shift Difference, etc.

Some of the pre-loaded deductions are 401(K), 403(b), 457(b), Cafe Plan, Child Support, ETT, Flex Plan, Garnishment, HSA (EM), Life Insurance, Loan, Medical Insurance, NJDI, NJFLI, PASUI, Reimburse, RITDI, Roth 401K, Roth 403b, SARSEP, Savings Account, Simple IRA, UI/WF/SWF/HC, Uniforms, Union Dues, United Way, WA L&I, etc.

When it comes to entering employee hours in payroll software, you can enter in a spreadsheet-style window or import hours directly from a spreadsheet or time clock solution.

After processing the payroll, you can print MICR-encoded checks on blank check paper or the payroll software will create ACH-formatted files for Direct Deposit which you can use via a bank or web-based deposit service for all Employer and Employee payments. You can even email pay stubs in PDF format.

The reporting functionality in CheckMark Payroll Software is quite robust. You get access to 40+ reports that can be viewed on-screen, printed, and saved as a text or .xls file. Some of the reports you can generate are Employee Information, Employee Earnings, Employee Paychecks, Incomes & Deductions, Department/Jobs, Employer Payment, Federal Taxes, 940 FUTA Tax, Employer Payment, Federal Taxes, State Taxes, Local Taxes, W-2 & W-3 Statements, etc.

CheckMark Payroll can be integrated with MultiLedger Accounting software, QuickBooks, Sage 50, MYOB, and many more popular accounting systems.

You can print completed Forms 941, 940, 944, 943, W-2, and W-3 forms on blank paper and pre-printed forms. You can also E-file W2s & W3s to the SSA and most states at the yearend.

CheckMark Payroll Software is compatible with Mac and Windows Operating Systems. Being a desktop payroll software, your sensitive payroll data will be saved on your local computer. Your employee and payroll records will be safe and secure.  CheckMark Payroll has a built-in add-on for cloud backup wherein you can save your data to CheckMark Cloud with a stroke of a button.

The software comes with two integrated support plans – Pro and Pro+. You can choose the best one that meets your needs or is right for your business. If you have any questions related to small business payroll, our US-based knowledgeable support team is always ready to help you. You may reach us by phone, email, or fax.

CheckMark Payroll is always up-to-date with the latest tax tables and Forms from the IRS and all 50 states.

The low cost of payroll software will help you save hundreds or thousands of dollars over the year. There is no monthly fee or set-up fee. All you need to do is purchase the payroll software for $509 and you are good to go for the entire year. No hidden fees or long-term contracts. The annual update price is minimal, which our customers consider a minor expense related to the importance of running an accurate and efficient payroll. We monitor IRS tax forms and state and federal tax tables on your behalf and keep payroll software up to date so you have complete peace of mind.

CheckMark Payroll Software is a really easy-to-use do-it-yourself payroll software. You don’t need any formal training and with our Payroll Manual and Customer Support, you can get started in a matter of minutes.

How to Do Small Business Payroll Using CheckMark Payroll Software

To get started, you need to download the free 60-day trial of CheckMark Payroll Software. With the trial software, you can run 4 payrolls free of cost.  Once you download the payroll software, install it on your local computer.

Setting up a company and adding employees

Once installed, under the File menu, click New Company. You have the option to copy company setup data. Enter a name for your company data files and click OK. After saving, the path to your company data files will appear at the bottom of the Commands screen. Only the Company Information button will be available.

Company Information:

Click Company Information and complete the fields.


You can add up to 99 departments. Refer to the Payroll Manual for more details.

Federal Tax Values:

Check that the year shown is the payroll year you are running. Nothing else to do here. Always install the latest version of CheckMark Payroll Software to be sure your federal tax tables are up to date.

State Tax Values:

Setup is required for all employers even in the states that do not require state withholding. Check the Load Latest Table button. Select all the tables for your state or state. Click OK.

Local Tax Values:

Use this button if you have a local income tax or if you are a California employer. Click Load Latest Tables. All California employers should click Load Latest Table and select “CASDI” to set up SDI.

Hour Categories:

Click Add From List and select Regular Hours and all categories that apply to your company.

Additional Incomes:

You can create a company menu of up to 20 additional incomes. Each employee can have up to 4 additional incomes in addition to 1 salary and 4 hourly incomes. Click Add From List for a list of templates that you can customize to fit your needs. You can also create your own by clicking the New button.

There are several calculation methods. Using the Variable Amount calculation to manually enter an amount later while running a payroll.

You have the option of setting the Fixed Amount at 0.00 and entering the exact amount per employee later as you assign incomes to the employees.


In addition to the standard payroll deductions, each employee can have up to 8 customizable deductions, and you can create a company menu of up to 30 deductions.

Click Add From List for a list of templates that you can customize to fit your needs. You can also create your own by clicking the New button. If you plan to manually enter the amounts when running each payroll, use the Variable amount calculation.


Enter the data for each employee. To learn more about importing an employee data file, please refer to the Payroll Manual.

Enter employee records using the employee tabs. The menus that you built during setup will appear as Company Categories under the Income, Deductions, and Accrued Hours tabs. Assign categories and customize as needed for each employee. The Accrued Hours tab helps you track hour categories such as vacation time and sick time.

The YTD tab shows the year-to-date totals. Before running your first payroll, you can enter your payroll history as of the end of a quarter. Please refer to the Payroll Manual for details.

Calculating a Payroll

Now that you have completed the company setup, you can quickly run a payroll.

Enter Hours:

All employees will appear on the left. The categories you selected under Hour Categories during the setup will appear at the top. Hourly employees are noted with a >. Enter the employee hours for the different categories and click Save.

Calculate Pay:

You can Calculate All, or calculate one employee by highlighting that employee and clicking Save. Employees listed in green are calculated and ready for the next step. If you want to re-calculate, highlight that employee and click Undo. You can create a paycheck for one employee by using Create Check. Or go to the next step to create payroll checks.

Review/Create Paychecks:

Only the employees who appear in the window will receive a paycheck. If there is a problem, return to Calculate Pay and make the necessary changes. To complete the payroll, enter the Next Check # and click Create.

Print Paychecks:


You can print checks as often as you like, so feel free to run a test on plain paper. You can use pre-printed checks or MICR-encoded blank check paper.

Use the Default setting or select Top, Middle, or Bottom Check to format your check paper. Click Edit to reposition print fields or suppress certain print fields for the custom formats. With the Edit window open, the fields with red letters will not print. Double-click a field to switch printing on or off. To reposition a field, highlight the field and drag.

Printing MICR encoding requires a laser printer. Complete the bank information fields and check Print MICR to turn it on or uncheck to turn it off. In addition to printing paychecks, you can also set up Direct Deposit. See the manual for details.

Modify Paychecks:

If a paycheck is incorrect, you can Modify a field, Void a check, or Delete a paycheck entirely.

Best Time to Switch Payroll Software

The best time to purchase payroll software is when you are just starting out a business or when you hire your first employee. When you are switching, then year-end or quarter-end is considered to be the most advantageous.

However, by switching at the beginning of the year, you don’t have to deal with collecting information from your previous payroll software or payroll service provider. You just need to start fresh for the new year – 2024.

If you are switching payroll software in the middle of the year, then you have to gather all your year-to-date information from your previous provider and import it into the new software.

Bottom Line

CheckMark Payroll has been awarded among the Top 10 Payroll Software Companies in the USA by HR Tech Outlook Magazine.

CheckMark Payroll is the most simple, flexible, and affordable alternative to cloud-based / online payroll software or online payroll services providers – Gusto Payroll, QuickBooks Payroll, Quicken Payroll Software, OnPay, Sure Payroll, Patriot Software, ezPaycheck payroll software, Square Payroll, Xero Payroll, Sage Intact, Payroll 4 Free, ADP Payroll, Paychex, Medlin, etc.

As a small business ourselves, we understand the unique payroll needs of small businesses that make us an ideal choice. We consider CheckMark Payroll as the best payroll software for small businesses in the market that not only saves the time of small business owners but also saves a considerable amount of money in the long run.

With CheckMark, you can manage payroll with ease and accuracy.

Download the free trial today and experience the power of CheckMark Payroll.