Small Business Payroll Management: A-Z Guide

Have you recently started a small business? If you need help with payment processing, new employee onboarding, and filing taxes, check out this small business payroll management guide.

Anja Simic
Written by Anja Simic
September 21, 2021
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Small business owners usually juggle multiple aspects of their business: developing the company, working with clients, hiring and supervising employees, and managing independent contractors. In between all of those tasks, they need to find time for doing payroll as well.

Even the basic payroll tasks can be time-consuming and complicated for any business owner. To make small business payroll management easier for you, help you save time, and show you all your payroll options, we created this detailed overview with a specific, step-by-step guide to small business payroll.

Small business payroll: the basics

Contrary to what it sounds like, payroll is not a simple act of paying your employees. It covers many more aspects, such as compliance with federal and state laws and paying taxes. Along the way, there are many decisions about the payroll process that small business owners need to make.

However, if outsourcing payroll services isn't an option at the moment, this guide will show you how to do your own payroll.

Employer Identification Number (EIN)

Before you take any steps or make any decisions about the best payroll service for your small business, you will need to register as an employer and obtain an Employer Identification Number - EIN. The IRS assigns a unique nine-digit number known as EIN to each business as a way to identify the company. Think of the EIN as a Social Security Number for employers. The EIN will be required on many payroll documents, so getting it is step zero for all payroll-related questions.  

You will need an EIN if your company:

  • has employees or is operated as a corporation or partnership;
  • deals with trusts, estates, farmers' cooperatives, or non-profit organizations;
  • withholds taxes on income other than wages for a non-resident alien;
  • files the following tax returns: Employment, Tobacco, Alcohol, and Firearms, or Excise;
  • has a retirement plan for self-employed persons (a Keogh plan);

Depending on the state you work in, make sure to check whether you need a state EIN on top of your federal EIN as well.

Registering for EFTPS

You can only make tax deposits for 

businesses using the Electronic Federal Tax Payment System (EFTPS). Before you start paying taxes, it's necessary to enroll in the EFTPS, which you can do on their website. You can pay taxes either by direct deposit for free or via credit card, with some fees attached.

Salary status

The essential step in defining the status of your employees is worker classification. If you are working with independent contractors and have employees, it is crucial to classify them correctly. To avoid misclassification penalties, make sure to report your employees to the IRS.

Next up is the salary status of your employees, as well as their exemption status. It would be best to determine which of your employees will have a fixed salary and which ones will have a wage.

Generally speaking, those who have wages are non-exempt, which means you need to pay them minimum wage and overtime. Exempt employees are not eligible for overtime pay, and they hold exemp

t positions, such as executives. To be exempt, salaried employees need to earn at least $455 a week or $23,660 a year.

Pay period and payment methods

There are several ways to structure the pay period and payment methods for your employees.

You can choose one of the four common payroll schedule  options and pay employees:

  • weekly
  • biweekly
  • semi-monthly
  • monthly payments

Sometimes, your full-time employees, who 

have a fixed salary, will have different paydays than your hourly employees, who get paid based on number of hours they've worked. It's critical to keep timesheets in order and track working hours accurately so you can calculate employee wages. Always double-check the data before making any final payroll calculations.

Although every employee prefers a specific pay schedule, make sure to base the payday decision on your cash flow and other factors that make payroll easier for you as an employer.

The usual payment methods are either a paycheck, a direct deposit into the employee's bank account, payroll card, o

r cash.

Employee information collection

Before you can start managing your payroll, there are some final forms and information about employees you need to collect. All your employees need to fill out Form W-4, which is known as Employee's Withholding Certificate. This form is used to estimate the amount that will be withheld in payroll taxes for the employee.  

In addition to the W-4, all your new hires need to fill out Form I-9, or Employment Eligibility Verification. After the new employee affirms their employment verification, the employer needs to check all the provided documents and confirm the verification on Form I-9. In short, the I-9 needs to be filled out by both parties.  

Finally, make sure to gather information such as deduction amounts for health insurance and retirement plans since they will be crucial for running payroll.

Workers' compensation insurance

Workers' compensation is an insurance type

 covering the medical bills and expenses arising from an injury on the job. In most US states, this insurance is mandatory and paid by the employer, but its rate can vary between states. Nationwide, the average workers' comp rate is 1.85% of the employee pay.

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Payroll taxes

As an employer, you pay several employment taxes when you run payroll. We advise all business owners to create and keep a tax calendar for their different tax deposits, for it will make tracking your obligations easier. Now let's break down the payroll tax payments:

FICA taxes

Federal Insurance Contributions Act (FICA) is the tax that funds Social Security and Medicare benefits. The employer pays FICA taxes, but the costs are split between the employer and the employee. When paying FICA taxes, you deduct the employee's half from their paycheck. The FICA tax rate is 15.3% of the employee's pay - 12.4% for Social Security and 2.9% for Medicare.

This calculation means employers pay 6.2% for Social Security and 1.45% for Medicare for their employees. However, both the salary or wages you pay your employees and your portion of the FICA tax are deductible expenses for the business. You can claim this deductible on the annual tax return.

Federal Income Tax

Employers need to withhold income tax from their employee's paycheck and then pay that tax to the IRS. You can calculate the withholding amount by checking their Form W-4 and choosing between the percentage method and the wage bracket method.

Neither method is simple, but the wage bracket method is more prevalent among small business owners. It would be best if you used IRS's Publication 15-T and the wage bracket method table. Find the values corresponding to the wage of each of your employees. Then, check their W-4 form to see if they file taxes as married or single, separate or jointly, and the number of claimed allowances they entered on the form. Use the instructions from Publication 15-T to calculate the exact amount to withhold from each employee's gross pay.

Employer taxes

Federal Unemployment Tax Act (FUTA) is an employer-paid tax that helps fund unemployment insurance and state employment agencies. It is sometimes known as the Social Security tax or the Medicare Tax. This tax is not withheld from employees' paychecks and is the expense of the employers.

If you paid more than $1,500 during one quarter to employees or had one or more employees for 20 weeks in a calendar year (whether full-time or part-time), you will need to pay FUTA. The FUTA tax rate is 6% before the state tax credits; this sounds like a significant amount, but after state tax credits, you can end up paying as little as 0.6%. FUTA also only applies to the first $7,000 of the employee pay for one quarter.

However, some US states cannot claim full state credit due to their outstanding loan balances. Make sure to check the tax credit of your state here. FUTA is paid quarterly, but only if you owe more than $500 in unemployment taxes. If you owe less, you leave the payment for the next quarter and then submit it using Form 940.  

Apart from FUTA, there is also the State Unemployment Tax Act - SUTA. These are the state unemployment taxes, and their rate, payments, and bases vary depending on the state. Make sure to keep up to date with paying SUTA tax according to your state legislation.

State and local taxes

Each state and local administration have their own taxes, including state income tax. Every small business owner should check their state and local tax authorities' website to check which taxes they collect and how much they amount to.

*Important note: Due to the Covid-19 pandemic, the United States President released an executive order that contains a payroll tax deferral for the period between September 1, 2020, and December 31, 2020. Find out more about the deferral here.

Choosing a payroll system for small businesses

Once you have registered with the IRS and the relevant state agencies, it is time to choose the model of running payroll for your business. There are three models to choose from:  

Manual payroll

Manual payroll processing essentially means managing payroll yourself. It is undoubtedly the most cost-effective method of the three, but it's also the most time-consuming one. Most business owners have enough on their plate without the taxes, documents, and procedures related to payroll. And even those who make time for these tasks eventually find out they are just too complicated. Mistakes can always happen, and that can lead to IRS penalties. Time is money, so unless you are a small business owner who happens to be a payroll expert, we don't recommend managing your own payroll. Of course, if your business is growing, you can always hire a payroll manager or an in-house accountant to run payroll.

Payroll software

Payroll software is an increasingly popular option for small business payroll. There is a multitude of software options ranging from desktop and mobile apps to online payroll solutions with multiple add-ons that enhance your experience.

The benefits of using online payroll services are plenty, but one of the most important is versatility. These solutions are typically user-friendly and can be used either in-house or by professionals, so business owners can always keep up to date with their payroll.

When choosing your payroll software, make sure to consider the nature of your business, the number of employees, and your budget for this expense. There are different payroll features to consider, such as automated tasks, like time clock functionality that helps you track your employees' hours automatically instead of manually.

Payroll plans and pricing come in ranges. Make sure to think carefully about your needs. Investing in payroll software can seem hefty at first, but the peace of mind that comes with neat payroll is worth every penny, especially when you get a comprehensive payroll report with all the data in one place: your employees hours and wages, payroll taxes, deductions, tax liabilities, and more.

Here are some of the most popular options:

  • Quickbooks Payroll Software

Quickbooks (some may know it as Intuit) is an accounting software often used by businesses in the US. Its features are diverse and cover accounting, tax filing, tax deduction, tax due dates, gross and net pay, cash flow management, and payroll. Some plans even calculate income tax withholding and offer tax penalty protection.

  • Deel

Deel offers contracts, onboarding, and payments for companies hiring independent contractors or international employees. Features on Deel include contracts compliant with local labor laws, payments in 150+ countries, and automated tax forms collection.

  • Gusto

Gusto is a platform offering full-service online payroll and beyond even with its Core plan. The platform has solutions for onboarding new hires, time tracking and employee benefits tools, and access to human resources experts for questions and advice.

  • Paychex

It's a suitable payroll and HR solution for small businesses and startups with up to 50 employees. Paychex has great customer support and it's cloud-based, with labor compliance tools and quote-based pricing.

  • OnPay

OnPay offers plenty of useful features packed in easy-to-use software. It has an accuracy guarantee and offers help on weekends in case of emergency. With OnPay, you can enjoy an automated onboarding flow and other HR tools.

  • Patriot Payroll

Self-service software that supports businesses with 100 or fewer employees. Patriot Payroll offers a 30-day free trial so you have time to determine if it works for you. You can easily integrate it with other accounting tools.


Outsourcing: Payroll services

The final option is to outsource the payroll management to an accountant or even a Professional Employer Organization (PEO). It is more expensive than doing it by yourself, yet it saves a considerable amount of time, enabling you to focus entirely on other aspects of growing your company. It's challenging enough to run a small business; payroll management can be delegated to professionals.

If you choose this option, we recommend doing extensive research and finding payroll providers specialized in your industry. Ask around and look for reputable professionals with happy customers and long-standing relationships.

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Keeping payroll records

Payroll duties don't end with paying your employees and the respective taxes. Record-keeping is a crucial payroll step, spanning across a multitude of categories. Federal and state governments have rules about how long you should keep payroll information if they need to be reviewed by the Department of Labor, the IRS, or a state agency.  

Information such as employee time cards needs to be kept on file for at least two years, while payroll data (like pay stubs) needs to be stored for three years. Rules also mandate you need to keep employee information on file. This info includes full name, Social Security Number, total hours they worked each week, the total amount of wages paid to the employee for each period, etc.

Is that all?

Whether you decide to do payroll by yourself, outsource it, or choose a software solution, it is crucial to select an option that balances your company's needs, costs, and time. If you are looking for a trusted partner for international payroll, look no further than Deel.

Schedule a demo to learn how we can help you with payments and compliance in 150+ countries.

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