How to Manage Payroll: Steps and Tips for Store Owners (2023)

manage payroll

Not sure how to manage payroll for your retail business? Then you’re in the right place. 

Payroll is the total amount of wages you pay your employees for the work they’ve done in a set period of time—usually scheduled weekly, every two weeks/twice a month, or monthly.

But payroll is more than just paying accurate wages. You also need to:

  • Collect employee data
  • Calculate net pay
  • Report, withhold, and pay taxes
  • Stay compliant with tax and labor laws
  • Keep accurate records

Paying your employees on time is essential for team morale and employee retention.

But managing payroll is a huge responsibility for any store. It can be dry, time consuming, and stressful. Doing it right is important to keep employees happy and to make sure your business is compliant with local tax rules. 

This guide takes you through the payroll setup, tips to manage payroll, and pros and cons of each payroll system you can choose.

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How to manage payroll: 7 steps to follow

Here are the seven steps you need to complete to set up and manage payroll:

  1. Register for an employer identification number (EIN)
  2. Collect W-4s from employees
  3. Establish a payroll schedule
  4. Decide how you’ll pay employees
  5. Calculate gross pay per period
  6. Withhold and pay taxes
  7. File tax forms and submit employee W-2s

1. Register for an employer identification number (EIN)

You need an employer identification number, or EIN, to hire and pay employees. EINs are unique numbers, the business version of a Social Security number.

An EIN is also known as an employer tax ID or a federal tax identification number. You’ll use it to report taxes and other relevant information to the IRS.

Using the online application is the easiest and fastest way to register for your EIN. Your information will be validated during the online session, and you’ll receive your EIN immediately.

Alternatively, you can apply by faxing or mailing a filled out SS-4 form to the correct number or address. You will receive your EIN within four business days over fax, or within four weeks for mail-in applications.

2. Collect W-4s from employees

For every employee you hire, you must collect their Form W-4, also called an Employee’s Withholding Certificate.

Each employee has to submit Form W-4 no later than their first day of employment. This form lets you withhold the correct federal income tax based on factors like marital status, dependents, other jobs or income, and deductions.

Make sure the employee signs the form; if they don’t, the form isn’t valid.

Your employees can complete and resubmit a new Form W-4 whenever their personal or financial circumstances change, and the IRS issues a new W-4 every year. Both are great reasons for employees to review their Form W-4 annually—feel free to encourage them to do so.

3. Establish a payroll schedule

Payroll schedule refers to how often your employees get paid. Common payroll schedules include:

  • Weekly: once a week (52 paychecks per year)
  • Biweekly: once every other week (26 paychecks per year)
  • Semimonthly: twice a month (24 paychecks per year)
  • Monthly: once a month (12 paychecks per year)

There’s no federal law that regulates how often you should pay your employees, but each state has its own law around the minimum pay frequency.

For example, in Arizona you have to pay your employees in intervals that are a maximum of 16 days apart (semimonthly), while Oregon and North Dakota require one monthly payment as a minimum. Make sure to check the state payday requirements when defining your payroll schedule.

When choosing the best pay period for your store, consider these three factors:

  • Cost and time: weekly is the most expensive, monthly the least.
  • Employee preferences: weekly is preferred by hourly employees, biweekly is favored (and how most employees in the US get paid), and monthly is least preferred.
  • Payroll and accounting logistics: weekly is most difficult, biweekly can be complicated, while semimonthly and monthly are straightforward and easy.

4. Decide how you’ll pay employees

The common methods for paying employees are direct deposit or a paycheck. You may decide to offer only one option or to let your employees choose their preferred method of payment. Regardless, figure it out during the hiring process and make sure you have all the information you need so you can pay employees on time. 

💡 PRO TIP: With Shopify POS, you can assign different roles and permissions and set boundaries on what store staff can do in your POS system without manager approval—like changing a product’s price or applying a custom discount to a sale.

5. Calculate gross pay per period 

Gross pay is what your employees make before taxes and withholdings. Calculating gross pay for salaried employees is simple. Divide their annual salary by the number of pay periods to determine the gross pay per paycheck. For hourly employees, calculate the total hours they work per pay period and multiply it by their hourly rate. 

6. Withhold and pay taxes

You have to withhold employment taxes from your employees for every pay period. The amount you withhold from each employee depends on the amount they earn and the information from their Form W-4.

These taxes include federal income tax withholding and Social Security and Medicare taxes.

Here are some resource to help you calculate, withhold, and pay the right taxes:

You can also help your employees understand their tax withholding (and their net or take home pay) by encouraging them to use the tax withholding estimator.

7. File tax forms and submit employee W-2s

Use Form 941 to file your quarterly federal tax return. This form lets you report income taxes, Social Security tax, or Medicare tax withheld from your employees, and your employer’s portion.

Form 941 is constantly updated, so always reference IRS instructions before completing and filing the form.

Every year, you also need to file employee W-2 forms with the Social Security Administration. This is usually due by the end of January for the year prior—the most accurate deadline is always listed in W-2 instructions. The SSA encourages all employers to file their W-2 forms electronically, as it helps with speed and accuracy.

You’re also responsible for filing a FUTA return (federal unemployment tax) annually. 

Remember to keep an eye on your state and local tax regulations to understand your obligations and deadlines beyond federal taxes.

Tips for managing payroll

Now that you know how to set up and manage payroll, here are some key tips to make it a breeze to manage:

  1. Share a payroll calendar
  2. Maintain employee and payroll records
  3. Stay updated on tax laws
  4. Appoint a payroll manager
  5. Ask for employee feedback

1. Share a payroll calendar

A payroll calendar is a public, shareable calendar that outlines pay periods, pay dates, timecard due dates, payroll tasks, and holidays.

This will help your employees understand:

  • When they’ll get paid
  • The period they’re being paid for
  • Potential delays or changes in pay dates (for example, because of a public holiday)
  • Their deadlines for submitting timecards

Don’t assume your employees will know these dates by default. One survey revealed that less than half of employees ever had their payslip explained to them by their employer, and almost as many don’t understand the information on it. 

Why would it be any different when it comes to payroll dates? A payroll calendar will reduce any confusion (and back-and-forth emails with employees asking for information).

For you, a payroll calendar calls out key tasks to do, like depositing payments and filing tax forms, so you can pay your employees on time, every time.

"Your financial health depends on how you manage payroll," says Courtney Quigley, Business Reputation Consultant at Rize Reviews. "Manage it with a payroll calendar so you can keep track of important dates, holidays, PTOs. It will also help your staff determine cut-off dates and payday. Share the calendar with supervisors and managers of your store or stores so they can transparently share it with their teams."

2. Maintain employee and payroll records

As you hire help for your store, you’ll generate documents and records for each employee, including:

  • General information: employee name, address, SSN, date of birth
  • Tax forms: W-4, state W-4, other withholding forms
  • Pre-hiring records: job application, interview records
  • Time and attendance records: time cards, total hours worked (per day and week), time off taken, remaining time off
  • Payroll records: pay rate, total daily/weekly earnings, overtime earnings, bonus pay and commissions, benefits and deductions, contributions, expense reimbursements, raise documentation, pay periods, pay stubs

Federal law states you need to keep payroll records for three years, and payroll tax records (like unemployment taxes) for four years. Some documents, like retirement income and 401(k) plan details, you must keep for six years.

Make sure to check laws and requirements for payroll recordkeeping in your specific state, as they might be longer than federal ones. For example, the state of New York requires you to keep payroll records for six years.

You can keep paper copies of payroll records, or electronically store them on your device or using payroll software. In both cases, it’s crucial to keep employee and payroll records safe, as they contain sensitive, confidential information.

“Organization is key—it’s critical that you maintain squeaky clean payroll records,” says Will Lopez, head of accountant community at Gusto.

“There’s a lot to do each time you run payroll, including getting the employee withholdings right, and you’ve got to keep up with quarterly IRS reporting. Be sure to dedicate a secure place to keep up to four years of employee I-9 forms, W-2s, W-4s, state new hire forms, copies of all your filed tax forms, and always maintain the dates and amounts of all tax deposits, timesheets, and pay stubs. Different states have different requirements when it comes to record-keeping (even for employees who have been terminated), so staying on top of requirements and keeping your records clean and well maintained will make audits run smoothly—this will also help you spot issues before they arise.”

Organization is key—it’s critical that you maintain squeaky clean payroll records.

Will Lopez, Head of Accountant Community at Gusto

3. Stay updated on tax laws

Payroll mistakes can cost you hundreds or even thousands of dollars in penalties. You must stay up to date with tax laws and requirements to make sure you:

  • File and pay taxes on time
  • Process payroll adhering to both federal and state laws
  • Calculate and pay correct overtime
  • Keep complete and accurate payroll records

One challenge is keeping up with laws that get updated regularly. The other one is making sure you stay compliant if and when your store grows—like expanding into different states, hiring remotely, or working with a mix of full-time employees and part-time contractors.

To stay up to date, regularly check in with the IRS website, your state tax websites (for example, for California and for Texas), and tax hubs like the one from Deloitte.

4. Appoint a payroll manager

There’s a chance your payroll tasks will outgrow the time and energy you can dedicate to them. This might happen because you go from two to 20 employees, open more locations, or simply double down on the one store you have and the community you already serve.

In any of these cases, payroll may become stressful and overwhelming. Instead of losing sleep over it, consider appointing a payroll manager.

If you’re looking to keep your business small but need to offload payroll tasks from your plate, this could be a hybrid role for an existing employee, or a part-time freelance role.

And if you’re looking to grow your store and need more robust payroll support, you can hire a full-time payroll manager, an external accountant, or a payroll service. They’ll do it better and faster than you—and they’re professionals who keep up with payroll laws and regulations. 

“Payroll is complex, which is why you should assemble your Payroll Squad,” says Will. “The key players who should be involved in your payroll process are: a) your payroll provider, b) an accountant (or other financial professional), and c) an HR business partner. Once you assemble this powerful Payroll Squad, you should divide and conquer; each person will own a part of the process and help you manage and approve payroll.” 

The key players who should be involved in your payroll process are: your payroll provider, an accountant (or other financial professional), and an HR business partner.

Will Lopez, Head of Accountant Community at Gusto

5. Ask for employee feedback

Make your payroll a two-way communication street. Instead of assuming your employees fully understand how payroll works (and that they’re happy with it), openly ask for their feedback and questions.

You can prompt employee feedback by asking:

  • Do you have any questions or concerns around using or submitting time cards?
  • Would you like to better understand your payslips?
  • Do you have suggestions around payroll schedules?
  • Is our payroll calendar clear and easy to navigate? Is there anything missing from it?

Everyone in your company is affected by payroll, so everyone likely will want to participate. It will help you improve how employees get paid. You can use questions and feedback to create internal documents and FAQs explaining your payroll process and how it impacts employees.

💡 PRO TIP: Want to control which staff can count, receive, and adjust inventory quantities? Set roles and permissions to create boundaries on what staff can and can’t do when logged in to your POS system, like accessing its inventory management tools.

How to choose a system to manage payroll

There are several ways you can manage your payroll:

  1. Manual/DIY payroll
  2. Payroll software
  3. Hire an accountant (in-house or external)
  4. Payroll services

Each has benefits and potential downsides—here’s what you need to know about each.

1. Manual/DIY payroll

Do-it-yourself payroll is often the go-to choice for those running a store as a side gig, and for small store owners with no plans to grow and expand.

This payroll system means you, the store owner, manually collect all documentation; file taxes over the phone or online; make deposits; and keep payroll and employment records.


  • Cost-effective—you don’t pay for a service, tool, or another person to do payroll.
  • Lots of control and insights into your revenue, cash flow, and payroll expenses.


  • It’s time-consuming (small business owners spend up to five hours on payroll every pay period), and hiring even one more employee adds extra tasks to your already full plate.
  • You can make errors and pay significant fines if you don’t catch them on time.
  • It’s your responsibility to stay up-to-date on tax laws and regulations.

Manual payroll can be a great way to start managing your payroll, but it requires lots of focus, time, and energy to make sure you’re staying compliant.

2. Payroll software

Payroll software is a solution that streamlines and automates payroll.

You’re still in charge of managing the data that goes into the tool, but payroll software lets you store tax documents, file and send payroll taxes, deposit payments to your employees, and more, so you don’t have to do it manually.

“DIY works when you have a small team, but it gets unmanageable as you grow—not just because it’s time consuming, but it opens up room for error,” says Lanai Moliterno, CEO and founder of Sozy

“It can be dangerous. Using payroll software puts so much into automated mode and safeguards your time and business from lawsuits and expensive mistakes. It’s a small extra expense, but it pays off in the long run with the time you save and the peace of mind you get.”

Using payroll software puts so much into automated mode and safeguards your time and business from lawsuits and expensive mistakes.

Lanai Moliterno, CEO and founder of Sozy


  • You have lots of control and insight into data, reports, filings, history, and more.
  • Easy access from all devices thanks to being cloud-based.
  • Affordable, with many options priced under $40 per month.


  • You’re still liable for any errors—a payroll software provider doesn’t take over your responsibilities to file and pay taxes, pay employees, or keep records.
  • There’s a possible learning curve, depending on your platform of choice.

Payroll software like Gusto reminds you when payroll is coming up, lets you track time and approve time off, helps you stay compliant by notifying you of tax law changes, handles benefits deductions, and more.

For store owners using Shopify POS, there are plenty of apps to choose from in the Shopify App Store to manage payroll, scheduling, and time tracking. 

Here are a few popular options, in no particular order: 

3. Hire an accountant (in-house or external)

You can hire an in-house accountant or an external contractor to prepare your accounts, keep track of your finances, and manage your payroll.

If you hire internally, this person could manage payroll manually or use payroll software—both options work. If you hire an external accountant, they’ll have their own process and setup for managing their clients’ payroll.


  • Extra time and focus for you, as you’ll offload dozens of tasks and reminders from your to-dos.
  • Removes stress and pressure from you to stay up-to-date on laws and handle payroll yourself.
  • You’ll have a go-to person for all questions about finances, taxes, compliance, recordkeeping, and more.


  • Less control over your filings and documentation.
  • It can be costly and disrupt your cash flow, especially if you bring a full-time employee on board.

If you choose this option, be sure to spend sufficient time looking for the right person. Ask for recommendations from fellow store owners and entrepreneurs, look up reviews, ask for references, and take the time to confirm the person fits your needs.

4. Payroll services

Payroll services, or payroll management companies, are a way to outsource your payroll management to a team of professionals. They calculate your payroll, file tax statements, deposit payments to employees, process new hires, and more.


  • Zero stress on your plate, as you have a team of people handling every detail of your payroll management.
  • Enhanced assistance for businesses that grow and change rapidly, hire remotely, and/or operate stores in different states and countries.


  • Costly to start with, and can get even more expensive as you grow and need more support with payroll and compliance.

While they can serve businesses of all sizes, payroll services are usually best suited for medium and large stores, due to the scale of expertise and support they provide.

PAYROLL TIP: If you are looking for a quick way to create paychecks for your employees try Shopify's pay stub generator.

Manage payroll right: get started 

Set up and manage payroll in a way that works for your store and the way you’ve imagined its future.

With Shopify POS, you get a complete view of your incoming revenue and can manage all of your store’s outgoing fixed, variable, and mixed expenses—from the inventory you purchase to the amount you’re spending on labor based on your employee scheduling. Just install one of the payroll and team management apps in our app store to take control of your payroll, scheduling, and labor cost management today.

Additional research and content from Alexis Damen.

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Manage payroll FAQ

How do you manage payroll?

Payroll management involves calculating employee wages, withholding taxes and deductions, generating paychecks and direct deposits, and filing and remitting payroll taxes. To manage payroll, employers should use payroll software or outsource to a payroll service provider. The payroll system should be fully integrated with the company's accounting system, allowing for seamless data transfer. Employers should also stay up-to-date on payroll compliance regulations, including tax laws and labor standards.

Is managing payroll hard?

Managing payroll can be time consuming and challenging, but with the right tools and resources, it doesn't have to be hard. Automated payroll systems, payroll software, and professional payroll services are all available to help make payroll easier to manage.

How do small businesses keep track of payroll?

Small businesses typically keep track of payroll by using accounting or payroll software. This software can help small businesses track employee hours, calculate wages, calculate deductions, and process payments. Small businesses may also need to use a payroll service to help with tax payments and reporting.