Payroll Software for Retail Businesses: Top Picks and Why Your Store Needs It

Running payroll by hand for your retail business? Bad news—that’s a fast track to burnout. Without payroll software for retail, doing it all manually means late paychecks, a dissatisfied team, even IRS penalties. Just ask the 70% of small business owners who feel buried under taxes and timesheets.

That’s where payroll software for retail comes in. It keeps your team paid, your books tidy, and your stress levels low—like a super-organized assistant who always has your back.

Let’s get into what to look for in a great retail payroll tool. 

TL;DR: Best retail payroll software at a glance

Need payroll help fast? Here’s a quick peek at the best payroll tools for retail:

1. Homebase

2. Remote

3. Paycor

4. Patriot Payroll

5. Keka

6. Gusto 

7. Square Payroll

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What is payroll software for retail?

Payroll software for retail is a tool for store owners and managers that automates the process of paying people. Modern payroll software tracks hours, calculates wages (including things like overtime, commissions, and tips), and takes care of taxes. Some payroll providers even have POS payroll integration and link up with your scheduling system.

You know retail: Between the shifting schedules, high turnover, and juggling full-timers  with part-timers and seasonal workers—keeping payroll straight can get messy. That’s why payroll software for stores matters. 

When everyone’s calculations, taxes and deductions are handled for you, you have fewer errors, things run smoothly from clock-in to paycheck, and you win back more time to focus on your business.

7 Best payroll software solutions for retail teams

Whether you’re running a standalone boutique or managing multiple stores, there’s a retail payroll software tool that’s right for you. Let’s dig into the 7 best retail payroll solutions on the market.

1. Homebase
Best for small retail teams that need all-in-one scheduling, time tracking, and payroll.

• Homebase is tailor-made for busy shop owners who want everything in one place—run payroll, track hours, and schedule shifts without juggling multiple tools.
• Especially great for hourly teams and integrates easily with popular POS systems.
• Offers a free plan that includes basic scheduling and time tracking features
• Upgrade to an affordable paid plan to unlock full-service payroll: $39/month base fee + $6/month per employee. 

2. Remote
Best for retail businesses with international or remote employees.

• If you’ve got staff across borders, Remote handles your international payroll, compliance, and tax headaches for you.
• Great for retailers expanding into global markets or managing hybrid teams.
• Might be pricey if you're only hiring a few international team members or working mostly locally.
• Global Payroll starts at $29 per employee/month.

3. Paycor
Best for growing retail businesses that want advanced HR and payroll tools.

• Paycor gives you powerful HR features with your payroll software, helping you with recruiting, onboarding, and employee development.
• A great fit for mid-sized retail operations looking to scale and streamline everything.
• Some users say it feels overwhelming for smaller teams or those just starting out.
• Basic plan starts at $99/month + $5 per employee.

4. Patriot Payroll
Best for budget-conscious retailers who just want simple, reliable payroll.

• Patriot gives you easy-to-use payroll at a wallet-friendly price—great for smaller retailers or those just starting out.
• Doesn’t offer built-in scheduling or time tracking, so you’ll need to use additional tools to manage employee hours.
• Basic Payroll: $17/month base fee + $4 per employee per month
• Full Service Payroll: $37/month base fee + $5 per employee per month

5. Keka
Best for large or global retailers needing more advanced HR features.

• Keka combines payroll with robust HR management, making it a strong choice for bigger teams or stores with multiple locations.
• Especially handy if you want detailed analytics, employee tracking, and workflow automation.
• More complex setup and may be an overkill for small or single-location stores.
• Software review sites say that pricing starts at about $120/month

6. Gusto
Best for retail teams that want user-friendly payroll with built-in benefits.

• Gusto offers a smooth, modern payroll experience, making handling benefits and compliance easy.
• Especially great for retail businesses that want to take good care of their team without hiring an HR department.
• Pricing can add up quickly if you need full-service features for a larger team. The price might be a bit steep for small retail businesses.
• Simple Plan starts at $49/month base fee + $6 per employee/month

7. Square Payroll
Best for retailers already using Square POS who want seamless payroll integration.

• If Square is your POS system, Square Payroll fits right into your workflow.
• Pulls in timecards and sales data automatically, so you can run payroll with a few clicks.
• Compared to all-in-one platforms, the advanced HR features are a bit limited.
• Full-Service Payroll starts at $35/month base fee + $6 per employee per month

Key features to look for in retail payroll software 

Whatever kind of retailer you are, your ideal payroll software will check some important boxes. Here are the most important ones to think about:

Time tracking. If your payroll software isn’t synching instantly with your time tracking tool, you’re wasting a lot of valuable time. All-in-one retail payroll software instantly calculates pay rates, hours, breaks, overtime and PTO the moment people clock in, then updates your timesheets for payroll.

Commission and tip reporting. If your retail team earns more than just hourly wages, payroll software that can handle commission and tip reporting is a must. 

1099 + W-2 compatibility. Look for a tool that lets people fill out and e-sign tax docs during onboarding, then syncs them with payroll. No more chasing people down for paperwork or wondering about their tax info.

Compliance and tax filing tools. Spend less time stressing over forms and deadlines—the right retail HR software helps you stay compliant with labor laws and automatically files taxes for you.

POS integration. Look for a tool that syncs payroll to your point-of-sale system. No more manual data entry means way fewer errors.

Scheduling tools. Payroll software that includes employee scheduling can be a gamechanger. When hours worked flow straight into payroll, you can build shifts, track attendance, and make sure everything lines up come payday.

Mobile access. Pick a platform that works wherever you are—whether you’re at the register, in the back office, or on the go. Mobile access lets you manage payroll, schedules, and time tracking right from your phone.

Take payroll off your plate with Homebase 

There are tons of payroll tools out there for every kind of business—but not all of them really get what a small retail team needs. And even if they do, they sometimes come with a price tag that’s a bit too steep for a growing shop trying to keep expenses in check.

Meet Homebase!

Homebase hits the sweet spot for small businesses—way more affordable than the $150–$300 a month you’ll see with a lot of other payroll tools, and it still packs in all the features you actually need:

No more late-night math. Homebase automatically turns employee hours into wages and handles federal and state tax withholdings for you.

Payday made easy. The platform sends direct deposits, files your taxes, and helps you avoid late payments or surprise penalties.

Shrink your paperwork. Have your team onboard, e-sign, and store their payroll forms in the app—no scanning, no filing. Homebase automatically submits your new hire reporting, filing and distributing W-2s and 1099s.

Keep everyone in the loop. Built-in team messaging lets you share payroll updates fast, and you’ll even know when your team’s seen the latest notes.

Run the whole thing right from your computer or phone. Or put your payroll fully on autopilot—so you can concentrate on running your store.

The best part? As your business grows, Homebase goes beyond payroll. We help you hire, schedule, track time, and stay compliant—all in one simple app that grows with you.

Try Homebase free today and see why 100,000+ small businesses trust us to make their teams unstoppable.

Small business recruitment software FAQs

Do retail businesses need special payroll software?

Stores don’t have to use "retail-only" software, but retail businesses definitely benefit from payroll software that’s built with their needs in mind.

Retail businesses need software that can handle things like syncing with your POS, tracking schedules as they change, managing tips, and ensuring accurate tax filings. Choosing a payroll solution that understands the retail grind will save you time, reduce errors, and make payday a lot less stressful.

What is the best payroll software for small retail businesses?

For small retail businesses, the best payroll software is one that’s easy to use, budget-friendly, and built with hourly teams in mind—and that’s where Homebase really shines.

It’s not just payroll: it’s your all-in-one team management tool. You can track hours, run payroll, manage schedules, and even message your team—all from one place (even from your phone). It's way more affordable than a lot of the big-name options out there, which is a huge win for small shops trying to grow without breaking the bank.

Can payroll software handle tips and commissions?

Yes, good payroll software can absolutely handle tips and commissions—and for retail businesses, that’s a huge help.

‍Instead of manually tracking who earned what, the right software will automatically calculate tips, track commissions, and include both in gross pay. It will also make sure taxes are withheld correctly, keeping your store compliant with labor laws. 

Can I pay both W-2 and 1099 workers with retail payroll software?

Yes, today’s retail payroll software lets you pay both W-2 employees and 1099 contractors (in the same system). This is especially helpful in retail, where you might have a mix of part-time staff, seasonal workers, and contractors. Good software will automatically handle the differences in tax withholding, year-end forms, and payment schedules. 

How much does payroll software cost for retail businesses?

The cost of payroll software for retail businesses can vary quite a bit, but the monthly subscription fees for most payroll services range from $25-$200/month. This covers basic payroll processing and tax calculations.

Many retail businesses opt for all-in-one platforms (like Homebase, Gusto, or Square Payroll) that include time tracking, scheduling, and POS integration.

Some of these platforms (like Homebase) offer free plans with basic scheduling and time tracking, with full-service payroll as an affordable upgrade ($39/month base fee + $6/month per employee paid).

Does payroll software integrate with retail POS systems?

Yes, many payroll software platforms do integrate with retail POS systems, and it’s a big win for busy store owners.

When payroll syncs with your POS, it can automatically pull in employee hours, sales data, tips, and commissions. This means more accurate payroll, faster processing, and fewer errors. It also helps with labor cost tracking, making sure people are paid based on real-time data from the floor.

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