Unlike the predictable, consistent payroll process at companies that hire employees, every week presents new challenges for firms that work with contractors.

Employees usually work at the same location, keep regular hours, and earn the same rate week to week. But contractors may work different jobs, at different sites, for different customers, and at different rates. So for every worker, you’ve to sort out overtime, bonuses, reimbursements, and deductions in each pay cycle.

To cut back on this complexity and save time, more and more contractor companies are now using payroll software. In this article, read about the top eight payroll software platforms for contractors. For each, I’ve identified the best use case to help you find the right fit for your company.

Platform	Best for	G2 rating	Free trial	Starting price
Buddy Punch	Connecting payroll to scheduling and timekeeping	4.8/5	14 days	$12.99/employee/month
Roll by ADP	Small admin teams in charge of payroll	4.6/5	3 months	$5/employee/month
Inova Payroll	Technician bonuses and sales commissions	4.4/5	No	Contact for pricing
Square Payroll	Emergency callout and after-hours pay	4.2/5	No	$6/employee/month
Justworks Payroll	Paying staff on different schedules	4.6/5	No	$8/employee/month
CheckMark Online Payroll	Keeping payroll in-house as you grow	4.4/5	60 days	$5/employee/month
Wave Payroll	Keeping payroll and bookkeeping in one place	4.1/5	30 days	$5/employee/month
Payentry	Joint payroll–cash flow solution	2.6/5	No	Contact for pricing

1. Buddy Punch – Best for connecting payroll to scheduling and timekeeping

It’s not unusual in contractor firms for employees to move between different customer jobs. It’s good to see everyone’s schedule at head office at the beginning of the week, but you actually need accurate clock-in and clock-out data to work out what each worker is owed. This is the information gap that Buddy Punch is very good at filling.

Buddy Punch is a combined scheduling, timekeeping, and payroll app. Managers can use it to create schedules for their crews. Crew members can then see exactly when and where they need to be on any day. They can use the app to punch in and out on site, either with a PIN or QR code, with geofencing restricting punches to the job location.

Every time entry feeds back to Buddy Punch in real time, so the hours you need for payroll get built as the week goes on. At any point, crew members can fix missed punches or wrong entries in the app. Managers can also change punch data, approve unusual hours, or add time that wasn’t recorded.

This means that, by payroll day, the hours in Buddy Punch Payroll have already been checked by crews and their managers. If you still spot any issue, you can go into the timecard and correct it before anyone gets paid.

Once you’ve verified the data, the app works out everyone’s regular hours, overtime, double time, and PTO. You can then add bonuses and deductions to each person’s record before you approve the payroll.

Buddy Punch takes two or four days to process payroll, so you need to submit the run by the cutoff for everyone to be paid on time. If you use another payroll company, you can export the approved hours in the right file format for more than 20 supported providers.

Pros

• One app connects scheduling, timekeeping, and payroll, saving time and reducing errors on each run.
• Every clock-in and clock-out is recorded live, so employees and managers can check and correct timecards in real time.

Cons

• Crew members can access their paystubs on the website, but not on the app.
• Changing bank details requires an administrator to rerun onboarding for that staff member.

Pricing

Buddy Punch’s Starter plan costs $19 per month plus $5.99 per user per month on monthly billing. This falls to $19 per month plus $4.99 per user per month if you pay annually. The Payroll add-on costs another $49 per month plus $8 per user per month and is billed monthly. That brings the combined starting price to $68 per month plus $13.99 per user on monthly billing, or $68 per month plus $12.99 per user when the Starter plan is billed annually.

2. Roll by ADP – Best for small admin teams in charge of payroll

In smaller businesses, the people responsible for paying everyone’s wages have a lot to deal with, from chasing timesheets and sending out invoices to answering staff questions and dealing with customer problems. Roll by ADP is a good fit for companies with small back-office teams who need payroll done quickly and accurately.

I like how the app uses a ChatGPT-type interface, so instead of having to go through multiple menus, you can just type what you want to do in plain English. For example, tell the app you want to add a worker, change someone’s pay, add a bonus, or start payroll. It may ask a few questions to understand what you need done, then walk you through how to do it.

Another time-saving feature is how it fills in the week in advance — handy if your staff mostly work the same hours each week. You can still make changes, like adjusting an individual employee’s hours, bonuses, deductions, and so on. For example, if someone didn’t work on a particular week, you can remove them from that run.

Employees can view their own paystubs and tax forms in the app, as well as update their address, bank account, and tax withholding details. Admin can also use the chatbot to pull up a worker’s previous pay, a quarterly payroll report, or your year-to-date figures instead of trying to remember which report to open. These help you cut down on time spent resolving pay queries, reviewing payroll data, and finding information for audits or management requests.

Roll also sends payroll reminders and flags anything unusual, like one employee being paid much more than normal, so you can double-check the figures before processing the run.

Pros

• The chatbot-style interface is intuitive and makes the app easy to learn and use.
• In-built AI helps users by, for example, providing warnings on potential payroll errors.

Cons

• You can’t add or change a wage garnishment yourself, so you have to reach out to Roll by ADP’s team for help.
• Users need to log into the app on their phone before they’re able to log into Roll by ADP on a desktop or a laptop.

Pricing

Roll by ADP costs a base fee of $39 plus $5 per worker per month. The company offers a three-month free trial and doesn’t require an annual contract.

3. Inova Payroll – Best for technician bonuses and sales commissions

Inova Payroll is a strong option for contractor firms using ServiceTitan that pay bonuses or commissions to technicians and salespeople for:

• Securing the job while giving a customer a quote
• Selling additional services when the current contract uncovers another problem, or signing the customer up for a maintenance plan

Traditional payroll software can make adding a fixed spiff, sales commission, or job completion bonus to an employee’s wages complicated and time consuming. ServiceTitan handles this well by letting you set incentive rules based on the type of work, value of the sale, and more. When someone makes a sale, it works out the extra pay using those rules and adds it to what they’re owed.

ServiceTitan automaticaly sends each employee’s hours and incentive pay details to Inova. It also makes adjustments for weighted-average overtime, which is useful when a technician receives more than one type of pay during the week, like ordinary hourly wages and a maintenance-agreement spiff.

Before submitting payroll, you can check and approve the amounts for each staff member. They’ll usually receive their wages by direct deposit within one to two days.

Pros

• Hours, commissions, spliffs, and more are worked out in ServiceTitan and transferred to Inova.
• The tool applies weighted-average overtime for technicians receiving different types of pay during the same workweek.

Cons

• To access the most useful services, you need subscriptions to both Inova and ServiceTitan.
• ServiceTitan reports it can take up to six weeks to integrate with Inova and get set up for payroll.

Pricing

Inova doesn’t publish standard prices for its payroll service or ServiceTitan integration. Contact its sales team for a quote based on your employee numbers, payroll requirements, and other services you want to include.

4. Square Payroll – Best for emergency callout and after-hours pay

When home owners or businesses need a situation dealing with straight away, like no heat, no water, or a serious leak, they won’t stop calling until it’s fixed. These urgent jobs — common for plumbing, HVAC, electrical, and other service firms — can bring in extra cash, but you do have to pay higher wages to the technicians that go out on these calls

I found Square Payroll handles this well. It lets you easily set up separate jobs and wage rates for the same employee. For example, you can pay a technician their ordinary hourly rate for daytime service work and a higher one for any emergency night-time or weekend callouts they attend.

Square Payroll works out what each employee is owed using their recorded hours and the jobs listed on their timesheet, keeping their ordinary pay separate from their callout pay. Check the payroll preview and, if you spot that a technician clocked in under the wrong job title or pay rate, you can correct it.

The app automatically calculates a blended rate based on the different rates they earned during the week. This saves your team a lot of time, because getting the overtime rate right by hand can be tricky.

Pros

• The tool separates employees’ ordinary wage and emergency or after-hours callout pay rates.
• It uses a blended rate to calculate overtime for technicians who have worked at more than one hourly rate in the same week.

Cons

• Only the account owner can run payroll, so you can’t hand the whole job over to your back-office team.
• If you miss someone’s callout pay, you can send it by off-cycle direct deposit, but it takes four days to reach them.

Pricing

Square Payroll costs $35 per month plus $6 per person paid each month. There’s no annual contract, and the price includes full-service payroll and payroll tax filings.

5. Justworks Payroll – Best for paying staff on different schedules

Many contractor firms start as a one-person operation, with the owner gradually building out an hourly field crew who expect to be paid weekly. As you expand, you add administrators and service managers, who often want to be paid every two weeks or every month. I like how Justworks Payroll gives you the flexibility to set separate payroll periods for both types of staff.

First, add each employee and enter whether you’re paying them by the hour or on a fixed salary, how much they earn, and how frequently they need to be paid. For example, choose monthly pay for salaried staff and select the first payday. For your field crew, choose weekly pay.

Confirm that everything looks right with the future dates on screen and save both payroll schedules. Once you’ve set them, the app automatically runs the salaried payroll. For the field crew, you’ll need to enter and approve their hours before the deadline.

When you log in now, check the automatically updating calendar to see which payroll is due next and when staff will be paid. If two cycles fall in the same week, the app keeps them apart and processes them as two separate runs.

Pros

• The app automatically populates the calendar with future pay runs for both types of staff.
• Each pay run is processed separately, even if both fall in the same week.

Cons

• Any changes to payroll periods can’t be made in the app once you’ve set them up. For this, you need to contact Justworks.
• The app allows a maximum of two pay run cycles, so it won’t suit your needs if you need more.

Pricing

Justworks Payroll costs $50 per month plus $8 per employee per month. The price includes employee payroll, payroll tax filings, W-2 filings, custom payroll periods, and payroll reporting.

6. CheckMark Online Payroll – Best for keeping payroll in-house as you grow

At the moment, you, your bookkeeper or an administrator may be handling payroll comfortably. But as you grow in size, the volume of work increases, eating up more of your time. You may not need the services — or expenses — of an end-to-end payroll agency for some time, but you may want software to handle the calculations and paperwork for you.

CheckMark will do this for you at a much lower fee than an agency. It prepares the payroll paperwork you need, but you remain responsible for making the payments and sending the returns on time.

To get started, open their app and add each employee’s pay rate, tax details, deductions, and how you pay their wages. When it’s time to run payroll, enter the crew’s regular, overtime, sick, and vacation hours as you normally would. You could also import them from a tab-delimited file if you already keep the hours in a spreadsheet, or export them from your time-tracking app.

When you select the pay period and payday, CheckMark calculates each person’s gross pay, taxes, deductions, and take-home amount. I like how you can calculate pay for the whole crew at once or one employee at a time. That means you can process the normal run in one go, or deal with someone separately if they’re on a different pay schedule.

After you’ve approved the figures, CheckMark creates an ACH file that you can upload to your bank or ACH provider for staff you pay by direct deposit. For staff who don’t want to be paid electronically, you can issue or print checks.

The app can also work out what federal, state, and local payroll taxes you’re liable to pay. To access this feature, you need to set up the IRS, state agencies, and other organizations as employer payees. The system then creates the relevant payment checks or ACH payments. The app prepares federal tax reports and W-2 and W-3 files too.

Pros

• The standard service includes unlimited payroll runs, ACH files, printed checks, and W-2/W-3 preparation.
• Run payroll for the whole company at once or for one employee at a time.

Cons

• You or your bookkeeper is responsible for making payments, tax deposits, and payroll returns on time.
• To pay 1099 contractors, you need separate CheckMark software.

Pricing

CheckMark Online Payroll costs $20 per month plus $5 per active employee per month. The company offers a 14-day free trial. The base package doesn’t include 1099 filing, so you need separate CheckMark 1099 software, starting at $239 for print-only filing or $319 for e-filing.

7. Wave Payroll – Best for keeping payroll and bookkeeping in one place

Wave has a free basic bookkeeping app, with payroll processing available as a paid add-on. If you use the two together, Wave automatically records everyone’s gross pay, employer taxes, deductions, and net wages in your accounts after each pay run, so you don’t have to manually enter the figures into accounting software.

I appreciate how simple Wave Payroll makes the whole process. Start by entering each employee’s regular, overtime, double time, vacation, and sick hours. You can also add extra items like bonuses, commissions, allowances, expense reimbursements, benefits, and deductions.

When you’ve entered everything, make sure what’s on screen tallies with each employee’s timesheet so you’re certain everyone gets what they’re due.

Wave Payroll offers a payment window of three days, so if you want to pay everyone on Friday, for example, you’ve to submit everything by close of business on Tuesday. Payment is by direct deposit, and the app takes care of your federal and state tax payments and filings.

As soon as the run goes through, it adds the bookkeeping entries into Wave automatically. You’ll see the gross wages and employer payroll taxes as expenses, while net wages and payroll taxes awaiting payment appear under liabilities. When you pay wages and payroll taxes, Wave records those payments against the liabilities, bringing the balance back down.

Wave and Wave Payroll bring payroll, invoices, customer payments, and everyday business expenses to the same place. You don’t have to move figures between two systems or pay for separate accounting software just to keep the books up to date.

Pros

• Wages, employer taxes, and outstanding payroll liabilities are automatically recorded in Wave.
• Pay employees by direct deposit and make federal and state payroll tax payments and filings through the app.

Cons

• You may still need to assign some benefits and deductions to the correct charts of account.
• Individual jobs or cost codes aren’t available in the basic package, so more granular profit tracking isn’t possible.

Pricing

You need a Wave business account to use Wave Payroll, but its basic Starter accounting plan is free. Payroll costs $40 per month plus $6 per active employee and $6 for each contractor you pay. The 30-day free trial begins when you approve your first payroll. If you want the additional accounting features in Wave Pro, it costs $19 per month billed monthly, or $190 a year billed annually (bringing it to $15.83 per month).

8. Payentry – Best for a joint payroll–cash flow solution

For many smaller contractor businesses, cash flow is an ongoing challenge. Customers expect to pay in 30 days after completion, or once a milestone is achieved, but you’ve got to find the capital to pay wages and taxes in the meantime. For companies that want help with both payroll and covering short-term gaps in working capital, Payentry is worth considering.

Payentry is a standard and well-featured standalone payroll app. Its highlight is that its funding partner, Payro, can lend you the money if you’re not sure you have enough to cover the run or are looking for a little breathing room while you wait for customer payments to come in.

After you’ve entered everyone’s hours, pay rates, bonuses, and deductions in Payentry, it processes the payroll, sends employee wages by direct deposits, files your federal, state, and local payroll taxes, and handles any garnishments. It also prepares and files year-end forms for you.

If you find you’re short on cash, request the amount you need through Payro’s online platform. You can choose a repayment period of up to four weeks. Before accepting the offer, you’ll see the interest rate, any fees, the repayment date, and the total amount you’ll have to pay back. If your customer pays you faster than expected, you can settle the loan with no early repayment charge. The capital then becomes available for you to borrow again.

Payentry’s 2.6/5 G2 rating would normally mean I don’t include it in a comparison article. However, I decided to feature it because the score is based on just six reviews, and it solves a real problem many contracting firms face. However, I’d ask for a full demonstration and let a few employees test it before signing up.

Pros

• Pay wages and payroll taxes in time while covering gaps in cashflow with Payentry’s in-built financing.
• The tool handles year-end forms as well as payroll, meaning you’re covered from each pay run through to tax season.

Cons

• Subscription to Payentry doesn’t guarantee a funding line from Payro.
• Interest rates start at 1.5% per week, so accessing funding regularly could quickly become expensive.

Pricing

Payentry doesn’t publish its costs or rates online. Contact their sales team for a customized quote. Payro offers approved businesses up to $500,000 in payroll funding, with rates starting at 1.5% per week.

Feature comparison

Platform	Payroll tax filing	Employee self-service	Time tracking or hours import	Payroll or accounting integration
Buddy Punch	✅	✅	✅	✅
Roll by ADP	✅	✅	✅	❌
Inova Payroll	✅	✅	❌	✅
Square Payroll	✅	✅	✅	✅
Justworks Payroll	✅	✅	❌	✅
CheckMark Online Payroll	❌	❌	✅	✅
Wave Payroll	✅	✅	❌	✅
Payentry	✅	✅	❌	✅

How I chose the tools on this list

The most important prerequisite for inclusion in this article was the ability to run payroll for W-2 employees. I treated being able to pay independent 1099 contractors as a valuable bonus, because many contracting firms rely on independent contractors for specialist work or extra help when business picks up.

I identified over 30 that could do both and then started researching each platform. I then shortlisted eight, based on the following:

• How easy it is to collect, check, and enter employee hours, rates, expenses, bonuses, and other payroll items
• How easily managers and staff can check their hours and verify them before they reach payroll
• What employees can complete or retrieve themselves, such as onboarding forms, paystubs, or tax forms
• How many manual entry and spreadsheet-related tasks the app simplifies or eliminates

One key factor in shortlisting was ease of use. I’ve seen how many businesses have struggled to roll out software that’s overly complex and unintuitive. Your best bet is to choose an app your staff will pick up with minimal learning, so that you get the benefits you want.