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Certified Payroll Software for Small Businesses

Certified payroll software is different from standard payroll software. You’ll need to use certified payroll software if you’re paying contractors on public works projects or government-funded construction projects.

As a small business owner, encountering a certified payroll request can be confusing. Today, we’re going to make life easier for you by listing the best certified payroll software for small businesses:

If you need payroll software, Intuit Enhanced Payroll is exactly what you need. Intuit also offers a 30 day free trial and its only $2/ per additional employee.

What is Certified Payroll?

First, let’s talk about what certified payroll is and why you might need it.

Certified payroll reports are typically required for workers on certain public works projects. When projects are publically funded, the contractor is typically required to pay a prevailing wage (also known as a Davis-Bacon wage) for workers on that job. Then, for each payroll period, that contractor is responsible for creating a certified payroll report. This payroll report shows the exact wages paid to each worker.

Today, payroll software like QuickBooks Certified Payroll and others make it relatively easy to create certified payroll reports.

The payroll software programs listed below will work as substitutes for federal form WH-347, which is the form required for certified payroll. They also work as a substitute for federal form WH-348, which is the Statement of Compliance required after you’ve submitted form WH-347.

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The WH-347 form is required to list all of the following information:

  • A description of the company and the project
  • The employee’s name
  • The last four digits of the employee’s Social Security Number
  • The employee’s job classification
  • Hours worked by each employee
  • Rate of pay, gross wages, deductions, and net pay for that employee

As you can see, your existing payroll software or QuickBooks should already have most of this information stored – which is why creating a certified payroll report in your existing payroll software probably isn’t as hard as you think.

After creating a certified payroll report, an authorized official must print and sign the report to certify its accuracy. This is called the Statement of Compliance, or form WH-348. Once you’ve completed all of these steps, you’ve successfully created a certified payroll report.

There are some myths about certified payroll. Some people mistakenly believe they need to be a Certified Payroll Professional (CPP) and pass an exam before legally being able to file a certified payroll report. That’s not true.

Another important misconception is that certified payroll is the same across all 50 states. That’s also not true, as certain states require you to electronically file multiple forms.

In any case, you can use the certified payroll software listed below to easily create and submit certified payroll reports.

Intuit Online Payroll and QuickBooks Are Certified Payroll

Intuit Online Payroll and QuickBooks Certified Payroll are typically the best options for creating certified payroll. Intuit has a good online tutorial on their website explaining exactly how to create a certified payroll report in QuickBooks here.

With Intuit Online Payroll, all the information you need for a certified payroll report should already be in your payroll solutions. Intuit recommends using the payroll software’s time tracking to pay employees, and that you should create weekly timesheets.

Adding certified payroll reports to Intuit Online Payroll isn’t as difficult as you might think. Once you have created weekly payroll and time tracking, the certified payroll job will automatically appear on your paychecks.

After that, you just need to use the Reports menu (Reports > Employees & Payroll > More Payroll Reports in Excel > Certified Payroll Report) then follow the on-screen instructions to create a report.

Some of the key features of Intuit Online Payroll’s certified payroll software include:


Intuit Online Payroll is priced at $20 to $30 for the base rate, with an additional $2 per employee added on. Here’s how the three different pricing packages break down:

Basic ($20 per month + $2 per employee per month): Intuit Online Payroll’s most basic plan is the cheapest, but it doesn’t provide much in terms of payroll functionality. With Basic, you get paycheck generation and the ability to pay employees by checks or direct deposit. You do not, however, get payroll tax submission features or electronic W-2 form filing.

Enhanced ($31.20 per month + $2 per employee per month): The Enhanced version is the most popular Intuit Online Payroll plan. It gives you the ability to quickly file paychecks by entering hours, just like the Basic plan. However, the main difference is that the Enhanced plan also includes payroll tax forms and electronic W-2 form submission at year-end. Most business owners depend on their payroll software to take care of payroll tax forms and W-2 form submissions, which is why the Enhanced version is the most popular plan.

Full Service ($79 per month + $2 per employee per month): The Full Service plan is a unique plan that provides your business with a dedicated Intuit employee who will run your business’s payroll every period. There are two advantages of this plan: first, the employee does all the hard payroll work for your business. And second, this plan guarantees you against tax penalties (if you get a tax penalty due to a filing error, then Intuit will pay it).

Available in 12 Countries

One reason why Intuit Online Payroll is popular is because it supports businesses around the world. The twelve countries covered by Intuit Online Payroll include the United States, Canada, Australia, South Africa, France, India, United Arab Emirates, the United Kingdom, Singapore, Brazil, and Ireland.

Certified Payroll That Scales to Meet the Needs of Your Business

Intuit Online Payroll can easily scale to meet the needs of your business. Adding new employees is easy, and you can switch between plans whenever you like. Since some businesses grow when taking on government projects that require certified payroll, this can be a valuable benefit.

Ultimately, Intuit Online Payroll and QuickBooks make it fairly easy to create certified payroll reports.  Once again, you can just follow this tutorial here to learn how to create certified payroll reports in Intuit Online Payroll/QuickBooks.

However, if you need an additional certified payroll software system for your small business, then the next option on the list will integrate directly with QuickBooks to do that for you.

Certified Payroll Solution

A company called Sunburst Software Solutions creates an add-on for QuickBooks called Certified Payroll Solution that lets you run certified payroll reports. If you’re only using QuickBooks and not using Intuit Online Payroll (or if you’re using a payroll software that doesn’t allow certified payroll), then this add-on is your next best option.

Certified Payroll Solution has been around since the early 2000s. Today, the software integrates with QuickBooks Pro, Premier, or Enterprise. It also works with Intuit Basic, Enhanced, and Full Service Payroll – so even if you have Intuit Online Payroll, you can cut through the hassle and buy this add-on to make things easier.

Some of the things to note about Certified Payroll Solution include:

Works with Multiple Types of QuickBooks and Intuit Online Payroll

As mentioned above, Certified Payroll Solution works with all types of QuickBooks and Intuit Payroll subscriptions, including QuickBooks Pro, Premier, and Enterprise as well as Intuit Online Payroll Basic, Enhanced, and Full Service packages.


Certified Payroll Solution costs $395 for a company license. That license lets you install the program on as many computers as required and is available through online download.

Easily Creates Certified Payroll Reports

Certified Payroll Solution, as you may have guessed from the name, is very good at creating certified payroll reports. The company’s software lets you easily create WH-347 Payroll Certification Forms as well as the WH-348 Statement of Compliance. There’s no need to double enter employee data: the software syncs with QuickBooks to monitor your hours and employee information and provide accurate certified payroll reports in a shorter period of time.

Can Provide Multiple Types of Certified Payroll Reports

Certified Payroll Solution works with both union and non-union contractors. The software holds all important information about employees, including jobs, payroll wage items, and payroll deductions, in the “linked records” section (QuickBooks does not include this information here by default). When creating a certified payroll report with Certified Payroll Solution, the software will take this information and merge it its own built-in certified payroll information to create the final report (additional information includes ARRA, EEOC/Work Utilization, and Fringe Benefit Reports).

Sign and Submit

All you need to do after using Certified Payroll Solution is print it off and submit it or file it electronically. It’s a timely way to use your existing QuickBooks data to speed up the certified payroll creation process.

Ultimately, Certified Payroll Solution isn’t the only way to run certified payroll on QuickBooks, but it does make your life significantly easier. If you need to create certified payroll reports with forms WH-347 and WH-348, then Certified Payroll Solution can help – although the high fee can make it a costly option for small businesses, especially if they’re only working on one project that requires certified payroll.

Construction Partner

Construction Partner is integrated accounting software. Unlike the other two options on this list, it’s designed to replace QuickBooks in your business’s bookkeeping department – not supplement it. It also costs $6,000, so it’s only a good option for larger construction firms with complex needs and dozens/hundreds of employees.

Construction Partner is also specifically designed for construction firms (hence the name). Since many construction projects are public works projects filled by independent contractors, the construction industry typically produces more certified payroll reports than any other industry.

In any case, Construction Partner promises to provide simplified data entry, seamless integration, and easy certified payroll reports with Statements of Compliance. Some of the software’s notable features include:

Produce Everything from a Single Screen

With Construction Partner, you can perform all bookkeeping tasks from a single screen, like record employee time, equipment hours, service work, and more. You can also import your data from a spreadsheet or a third party time tracking program.

Calculates Everything

Construction Partner calculates everything that needs to be calculated when running payroll for construction firms. It calculates taxes, union benefits, pre-tax deductions, and burdens, for example.

Multiple Modules

If you want to make Construction Partner your primary bookkeeping software, then you’ll find plenty of add-on modules available to cover all aspects of construction industry bookkeeping. For example, you can add modules like Job Costing, Equipment Management, Service Billing, and Inventory. Best of all, your payroll timecard entry will share information with all other Construction Partner modules, reducing the need for double entry.

Meets Complex Requirements

From 401(k) plans to section 125S special pre-tax deductions, Construction Partner is specially designed to handle the unique challenges construction firm bookkeepers face every day.


Construction Partner pricing varies from firm to firm. The company’s website claims that you can expect to pay just over $200 per month for Construction Partner through their financing plans for a total final cost of $5,995. You’ll also need to pay an additional $895 per year for monthly fees (the first 90 days of maintenance are free).

As justification for that price tag in comparison to QuickBooks, here’s what the company has to say:

“Don’t waste another day managing your construction company using spreadsheets, QuickBooks® or software that just doesn’t meet your needs. We can even work with you to set up financing options for as little as $200 per month.”

In any case, you can schedule your Construction Partner online demo with a salesperson by filling out the form here.

Other Features

You can view Construction Partner’s full list of included features here. Some of the other notable features included in the software include:

  • Ability to add up to five direct deposit accounts for each paycheck
  • Online review of complete calculated payroll prior to check printing (“reduces errors”)
  • Tracks critical employee data, including re-hire, termination, birth dates, automatic tracking of hire, driver’s license, and work permit number
  • Detailed payroll registers that display pay/deductions for each employee along with summary totals by G/L account, pay and deduction codes, and tax deposits for the pay period
  • Magnetic media submission support, including the ability to submit state SUI quarterly reports and W-2s in MMREF format

Ultimately, Construction Partner is a niche software program catered towards construction firms that regularly complete jobs requiring certified payroll reports. Of course, it also has plenty of features beyond simply creating certified payroll – including job costing, estimating, accounts payable/receivable, general ledger, equipment management, service billing, purchasing, inventory, and labor compliance. It’s a complete accounting, bookkeeping, invoicing, and payroll software for construction firms.

About Johnson Hur

After having graduated with a degree in Finance and working for a Fortune 500 company for several years, Johnson decided to follow his passion by embarking on a path to the digital world. He has over 8 years of experience with large companies setting marketing strategy.

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