How to Choose the Best Payroll Software for Small Business

payroll software for small business

When it comes to choosing the best payroll software for small business, it can often feel like a daunting task. Unless you have experience, the thought of finding the best payroll software can seem intimidating, stressful and time-consuming.

If you’ve taken the decision to better focus your time on running your business, rather than deal with complicated spreadsheets and manual processes, then you’ve made the right choice. However, when it comes to choosing the best payroll software for small businesses, it’s important you find the right one. To help you with this process, we’ve put together a useful guide highlighting all the important qualities and factors that your payroll software should contain.

1. User-Friendly and Ease of Use

Changing from a paper-based payroll system over to a more advanced paperless payroll system should not require an extensive learning curve or time-consuming training sessions. Your small business needs access to software that offers a simple solution that doesn’t require you to jump through hoops to achieve it.

user friendlyIt’s important that multiple employees of your small business are able to use the software with ease, without the need for expertise in the field. This removes the need to hire a professional and keeps overall business costs low. When you are choosing payroll software, aim for software that’s smooth and can be installed on any computer. The easier a solution is to use, the higher its adoption rate and the faster you’ll realize your return on investment.

2. Simple and effective setup

It’s important that the right payroll software offers both a simple and effective setup. It should have the ability to import data from other software you may have been using, or if the manual entry is necessary, this should be quick and easy.

3. Security

Payroll handles some of the most sensitive information your business has, from bank account details, social security records, salary figures, etc. As such, properly securing this data is of the utmost importance. Failing to do so could make your business liable to harsh penalties. That means, when it comes to choosing payroll software for small business, security is an important aspect.

Make sure that you are aware of how the provider secures your sensitive information. The payroll software should be bonded, insured and hold high-security encryption. This means you can have peace of mind that the information is safe.

4. Features

The best payroll software for your small business will carry a variety of essential features to help make payroll a seamless process. These important features are listed below, and you should ensure your payroll software includes these.

direct deposit– Direct Deposit

When funds go directly into your employees’ bank accounts, it brings convenience, speed, alongside a lower risk of fraud, global deforestation and lost checks.

– Tax Compliant

When you pay yourself or your employees, there are a variety of payroll taxes that need to be considered. These include social security, income tax, Medicare, amongst other standard expenses. Good quality payroll software will help you to automate this function by deducting, and reporting the amount, then allowing you to report these funds to the appropriate vendor, whether it’s the local tax authority or state. If your payroll provider deposits taxes for you, then this eliminates stress for you about late payments or mistakes. Your payroll provider has you covered.

– Several Income Types

The best payroll software should allow for a variety of different incomes, including commissions, holiday pay, expense reimbursements, bonuses and any other benefits which are taxable.

– Variety of Deduction Types

It’s important your payroll software also has the ability to deduct costs such as dental, vision, medical and life insurance.

– Off-Cycle Payroll

Another factor is the convenience of off-cycle payroll. This feature will allow you to process an advance or final payment, distribute bonuses, or make a correction.

– E-File W-2s & W3s to SSA

A good payroll software will allow you to E-file W2s & W3s to the SSA and various states at no extra cost. This is a necessity, especially as your small business grows.

– After the Fact Payroll

After the fact payroll allows you to access the values of payroll that have already been issued. This helps ensure that you have full compliance reporting.

4. Features

Alongside these important features, it’s also important that your chosen payroll software offers these additional functions too: MICR check printing, 401K deductions, and the ability to process payroll for salary as well as hourly employees.

5. IRS Compliant


It’s very important that your preferred payroll software is integrated with the latest IRS taxes and taxes for all 50 states at local, federal and state level. These should be made available to you as soon as they are released. This ensures you are always up to date and minimizes any risk of mistakes being made with compliance.

6. Reporting

Reporting capabilities go hand in hand with tax compliance. You often find that these same agencies will require regular reporting of payment amounts. It’s also a requirement at the end of the year. To help ensure this process is seamless and mistake-free, the following payroll reports should be at your fingertips: W2, W3, SUTA, FUTA, wage summaries, employee earnings, Forms 940, 943 and 944. A good payroll software system will make this possible without complications.

7. Affordable

For many small business owners, the final decision of who they choose for payroll software is the cost. Your payroll provider’s pricing structure and services should be completely transparent so you know exactly what it’s going to cost you, based on how many employees you have and the services you select. The best payroll software will charge a one-time low fee with no setup fees or sneaky hidden charges.

It’s important that you can add unlimited employees and companies without additional costs. You should also be able to E-file W2s & W3s to SSA and most states, without additional costs. It’s important you can achieve all these things without extra charges because as your small business grows and develops, your payroll software should be able to handle more.

8. Support

customer support When you use a payroll system, you have control over your payroll. However, it’s important you don’t feel alone if you need help or assistance. A payroll software company that offers a strong support network will help you feel more comfortable and confident with running your own payroll.

Fortunately, many payroll systems offer customer support in one form or other. Depending on your business needs and requirements, you might factor in the type and level of support you will receive when deciding on payroll software for your small business. When choosing that level of support, you will want to search for a US-based support team who are knowledgeable, helpful and friendly. It’s important that they are accessible both through email and phone and that they respond in a timely manner.

9. Free Trial

When you are making an investment in your small business, it’s important that you can test that product, and ensure that it works well within your business. The best payroll software companies will allow you to test their product with a “Free Trial”. This typically comes in the form of 14 to 60 days. This allows you to get a feel for the system and helps you see exactly what you are purchasing. It will allow you to learn the system with a hands-on approach and run your first payroll at no extra cost to you.

10. Integrations

software partners

It’s never a good sign if you opt for a payroll provider who is unwilling to integrate or partner with other time clock software, and accounting software systems. These types of providers should be avoided. When a payroll provider’s system is easily integrated with other types of accounting and tax reporting software platforms, you are afforded more control, greater flexibility, and better results.

It allows for efficient business operations. It’s also important for the payroll provider to partner with benefits providers and comps to understand the needs and requirements of small businesses in order to provide the complete and best payroll package possible.

By automating your payroll, you are not only saving yourself the pain of mistakes, but you’re removing a huge administrative burden off your shoulders, which frees up time that is better spent on growing your business. The right small business payroll software is like having your own expert in-house and the good news is, CheckMark Payroll can offer you just that.

Our payroll software incorporates every single item we’ve included on the list above. CheckMark Payroll is ideal for small businesses because it was built with small businesses in mind. When you are choosing a company to work with, you want someone who has designed their Payroll software specifically for your size of business. We are aware of your unique needs, and we want to provide you with everything you need and at a brilliant price too.

CheckMark Payroll includes high-end features like MICR encoding, direct deposit, and handles unlimited employees and unlimited companies. It can also be used as a standalone system or integrated with a variety of popular accounting systems. Our US-based support team will be on hand to help with difficulties and provide advice quickly.

payroll software for small businesses

We’re passionate about providing small businesses with an alternative to spreadsheets and expensive, conventional, and manual payroll providers. Your small business is innovative and modern, so shouldn’t your payroll system be the same?

If you’re ready to switch your payroll to an effective and easy-to-use system that will grow alongside your business, then try CheckMark Payroll today. With our free trial, run first 4 payrolls free of cost. Get started today!