Best Payroll Software Solutions for Cleaning Businesses

Payroll might just be one of the biggest recurring hurdles of running a cleaning business. Especially if you have to keep track of things like hourly work, overtime, sick time, PTO, and more, it’s a struggle to ensure that you didn’t accidentally underpay (or overpay!) an employee.

Luckily, there are some great software options out there to automate this process for you, so you can spend time managing your business rather than trying to ensure you’re paying all the right amounts to your employees every week. 

In this guide, we’ll walk through why payroll software matters, what features to look for, and which tools work best for cleaning businesses. We’ll also share recommendations from our in-house cleaning experts on their experiences and any tips they suggest to make sure you pick the option that works best for your crew.

Why Cleaning Businesses Need Dedicated Payroll Software

There’s nothing that makes cleaning businesses require payroll software more than any other service business, but it’s just smart small business sense. 

Payroll software makes life easier for everyone, especially when it comes to doing things the legal and compliant way. Most good payroll platforms offer built-in guidance on tricky situations, like reporting new hires to the state (if you’re based in the United States) or handling wage garnishments. These situations come up for any business owner, and it’s a relief to have software that helps you do them correctly.

From both a compliance and convenience standpoint, payroll software is a no-brainer. Without it, you’re making things harder than they need to be, and you risk getting something wrong without realizing it. And, unfortunately, it’ll still be your responsibility if you do. 

How to Choose the Right Payroll Tool for Your Cleaning Business

Every cleaning business is different, so it’s important to evaluate the most important factors for your current situation. With that in mind, our cleaning business experts advise that you prioritize the following four factors:

• Straightforward pricing
• Easy time tracking
• Automated taxes and compliance
• Different payout options

Let’s jump into it.

Straightforward pricing

Sometimes, software comes with hidden fees based on what you choose to do with it. For example, watch out for platforms that look cheap up front but add fees for every payroll run, tax form, direct deposit, etc.

Easy time tracking

Your payroll tool should integrate with mobile time tracking, which most payroll software doesn’t directly offer. 

For example, if you were using QuickBooks with ZenMaid for scheduling, ZenMaid software would calculate weekly payroll based on scheduled and logged hours and export directly to QuickBooks, which you can then pay out to your employees.

Automated taxes and compliance

Tax rules change from state to state (and even city to city). A good payroll system should handle withholdings, file tax forms for you, send out year-end W‑2s or 1099s, and know when to apply certain rules or deductions.

Different payout options

Not everyone prefers direct deposit, so make sure that the payroll tool you choose offers different options. Direct deposit is the most popular (and often the easiest), but some cleaners prefer a paper check, for example, and this is especially important if you have a mix of long-term, part-time, and seasonal employees.

Referrals and reviews

Don’t underestimate the power of referrals and reviews from others! Make sure to check out what others are saying about the choices you’re considering by doing a few quick searches. 

For example, one of ZenMaid’s internal cleaning experts, Maria, used a no-name brand for well over eight years at her cleaning business. They were super affordable, never late in sending out payments, and, overall, a very easy platform, but they weren’t known at all by the broader market. The software came from a recommendation by another person, and it ended up being a choice Maria’s business never strayed from.

Top 4 Payroll Software Options for Cleaning Companies

Gusto — #1 overall payroll choice for cleaning businesses

Our experts unanimously recommend Gusto. Stephanie, a ZenMaid employee and owner of Serene Clean, switched from QuickBooks to Gusto around year three of her cleaning business being open. In her words, “I’ve never looked back.”

For starters, Gusto has phenomenal customer service. That’s the biggest difference between them and other platforms — Gusto’s team feels like actual payroll experts. If you start offering benefits and need to make deductions from paychecks, for example, having that expertise is a lifesaver.

Gusto also partners with other services to make benefits easy. For example, 401(k) programs can be offered through Guideline, which is one of Gusto’s partners. The same goes for health insurance. 

The reporting is also excellent, and there are lots of small added features that make the user experience really great. Additionally, based on what permissions you set, staff can log in and see everything they need at any time. 

Overall, Gusto is a five-star choice because it handles so much automatically, like new hire reporting, payroll tax calculations, and more.

Gusto’s pricing is as follows:

• Simple — $49 per month + $6 per person per month
• Plus — $80 per month + $4.80 per person per month
• Premium — $180 per month + $8.80 per person per month

Paychex

If your cleaning business is scaling fast and you want more than just payroll, Paychex might be a good option. It’s a full-service platform that includes payroll, HR, and benefits all rolled into one. 

Like Gusto, you get access to real payroll specialists, as well as tools for onboarding, tracking time, and managing compliance.

With that said, Paychex can be pricier than other options, especially for smaller crews. It’s a bit less intuitive so you’ll have to take some time to learn and get running, but if you’re building a larger team or want to streamline HR and payroll under one platform, it’s worth a look.

Unfortunately, if you want pricing, you have to contact Paychex directly (all of their pricing is custom).

QuickBooks Online + Payroll

QuickBooks is a popular choice for payroll if you’re already using it as your accounting software. Adding their payroll feature keeps everything in one place, which is handy — you can run payroll, track taxes, and automatically sync all those numbers into your books.

This is a good option for cleaning business owners who want everything connected, but unlike Gusto or Paychex, it’s not specialized in payroll. If your payroll needs are straightforward and uncomplicated, this is a good choice, but may require a lot of extra effort if you run into any complexities.

QuickBooks offers three pricing tiers:

• Payroll Core — $50 per month + $6.50 per employee per month
• Payroll Premium — $88 per month + $10 per employee per month
• Payroll Elite — $134 per month + $12 per employee per month
• There also more expensive tiers if you choose to bundle your payroll with bookkeeping. 

Wave Payroll (by Wave Financial)

Wave Payroll is part of the Wave software suite, which offers free accounting tools. It’s a natural choice for small or brand-new cleaning businesses that need to keep an eye on costs. The payroll add-on handles direct deposit, tax calculations (in certain states), and year-end forms like W‑2s and 1099s, but you can’t only use it by itself.

Also, it’s more bare-bones than other tools, and if you’re outside their “tax service states,” you’ll have to handle filings yourself. 

As of mid-2025, the cost for Wave Payroll is a $40 base fee plus $6 per active employee and $6 per per independent contractor paid.

How to Set Up Payroll Efficiently in 5 Steps

Once you’ve decided to go with a software solution instead of manual Excel or paper-and-pen tracking, here are the steps and tips we recommend.

1. Choose your payroll platform

Start by picking a payroll software that fits your business size, team structure, and how you prefer to operate. Our list above can help you narrow it down, and you can also turn to sources like Google, Reddit, Facebook, and more for recommendations based on your specific case.

2. Gather employee information 

You’ll need to collect some key details before you can run your first payroll:

• Employee or contractor info (i.e., name, address, Social Security number, or EIN)
• Bank account info (if using direct deposit)
• Completed W‑4s for employees and W‑9s for contractors
• Pay rates and job roles

3. Decide on a pay schedule

Will you pay your team weekly? Biweekly? Monthly? Set a regular schedule that works for your cash flow and stick to it. You’ll also want to decide how you’re tracking hours — whether it’s through your scheduling software (like ZenMaid) or something else that integrates with payroll.

4. Sync time tracking

If your cleaners are hourly, this is super important. Sync your scheduling or time tracking software with your payroll platform to avoid manually entering hours each pay period. 

Most modern tools offer integrations. For example, ZenMaid can export hours directly into QuickBooks or other payroll platforms.

5. Run payroll and automate the rest

Once everything is set, you’re ready to go. Before you hit submit, review the pay period, make sure hours and pay rates are correct, and confirm any withholdings. Once it’s live, your software should handle:

• Direct deposit (or paper check, if needed)
• Tax calculations and filings
• New hire reporting
• Year-end tax forms like W‑2s and 1099s

We also recommend to set up a recurring payroll run and reminders (which most software has nowadays).

FAQs

What’s the best payroll tool for cleaners with hourly workers?

For cleaning businesses with majority hourly workers, we recommend Gusto. It’s designed with hourly teams in mind, though it has options for salaried workers too, and makes it easy to run payroll weekly or biweekly, track hours, calculate overtime, and handle tax filings

Tools like QuickBooks Online Payroll and Paychex also support cleaning businesses with hourly payroll employees, but Gusto is our first choice because it’s so intuitive for both the business and employees.

Also, if you already use time-tracking software like ZenMaid, look for payroll platforms that integrate to avoid manual data entry..

Can I use payroll software even if I only pay contractors?

Yes — payroll software can help you keep track of contractor payment information, preferences, schedules, and more.

How much does payroll software typically cost for a small cleaning team?

As of 2025, the majority of payroll tools charge a base fee along with a per-employee or per-contractor rate. Here’s a rough breakdown based on current pricing:

On average, for a team of 3–5 cleaners, you can expect to spend $50–$100/month on a reliable payroll system.

Will payroll sync with accounting software like QuickBooks or FreshBooks?

Yes — most modern payroll tools offer integrations with accounting platforms:

• Gusto syncs with QuickBooks, Xero, and others
• QuickBooks Payroll integrates with QuickBooks Online (as you’d expect since it’s the same company)
• Wave Payroll works natively with Wave Accounting since they’re built together
• Paychex and others usually offer integrations with QuickBooks, but some may require setup or upgraded plans

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