Getting a payroll system in place for your small business can seem like a daunting and potentially expensive challenge.

While a large corporation might be willing and able to shell out some dough to a traditional full-service payroll provider like ADP, as a small business owner you simply can’t afford that luxury. And given the smaller size of your business, you probably don’t need all the bells and whistles a full-service provider offers anyway. You just want some automation and features that speeds up the payroll process, ensures more accuracy in paying employees and helps integrate payroll processes with other financial tasks, such as bookkeeping and tax preparation.

Luckily, cloud-based software options are expanding online, and staffing websites such as Upwork make it possible to contract with a professional bookkeeper at an affordable price.

Outsource It to a Professional

Payroll and taxes are a headache for any small business owner with way too much to do. That’s why small business experts like Gene Marks suggest you outsource it. “You’re crazy to do your own payroll,” says Marks. But how do you find someone to do it for you?  Google “payroll” and your location and you can quickly find a local service provider to take the payroll headache off your plate.

Get It Packaged With Accounting Software

Perhaps you want to tackle payroll efficiently by having it packaged in with your overall accounting software, which may even provide you with a discount. There are a number of relatively affordable options out there.


With the well-known accounting software Intuit QuickBooks you can track income and expenses, create invoices and estimates, sync bank accounts and apps, pay your employees and file payroll taxes.

As a bonus, many accounting firms already use QuickBooks which makes working with your accountant easier.

Cost: QuickBooks with enhanced payroll functions starts out at $30 per month, then increases to $60 per month.

FreshBooks (Combined With Gusto)

If QuickBooks has too many bells and whistles, FreshBooks—used along with a separate payroll software called Gusto—might be a more streamlined, and affordable, option for a startup.

FreshBooks is a cloud-based accounting software that offers many of the key services that small businesses need but not all the extras of more robust software.

For your payroll needs, FreshBooks integrates with add-on software from Gusto (formerly ZenPayroll).Gusto’s features include the ability to run payroll on a recurring pay schedule; automatic calculation, payment and filing of local, state and federal payroll taxes; and employee logins so your workers can onboard themselves and access pay stubs, W-2s, 1099s and more.

Cost: FreshBooks costs $17 to $50 per month, depending on the extent of the package. 


Looking for an even cheaper option that combines accounting with payroll? Business News Daily this year declared Wave as the 2016’s best free accounting software for small business, citing its ease of use and time-saving features such as setting up recurring bills and invoices and the ability to set reminders to help keep track of what has been paid or not paid.

Wave’s payroll software features include streamlined year-end filing, easy-to-understand tax liabilities tracking, a self-serve portal for employees, payroll reminders, direct deposit and check printing, 256-bit SSL encryption and automatic backup.

Wave’s features are best for the self-employed or businesses with fewer than 10 employees, Business News Daily noted. And while Wave’s accounting and invoicing software might be free,

Cost: Adding payroll to Wave’s free features costs extra: a base fee of $40 per month plus $6 per employee per month.

Just the Payroll, Please

If you’re just looking for an affordable online service to handle your payroll, there are options for that, too.


Paychex’s SurePayroll claims that users can get their payroll done in two minutes. The service includes direct deposit and online pay stubs for employees. Payroll taxes at the federal, state and local level are filed automatically, and W-2s and 1099s are posted online at year’s end for approval. Payroll can be run on any device, with no installs or downloads.

Paychex also offers an online product, Paychex Flex, that integrates payroll with timekeeping and human resources.

Cost: You can get a payroll quote on their website to find out pricing details specifically for your small business. 

Another online payroll service, OnPay, offers services including unlimited pay runs, onsite check printing and direct deposit. OnPay also handles tax payments and filing, and support is available via phone or email.

Cost: It has a base fee of $40 per month and $6 per month fee for each employee.

Gusto (formerly ZenPayroll)

Though it integrates with FreshBooks (as featured above), it can be purchased and used separately.

Cost: It offers a $40 per-month base price, plus $6 per month per employee.

Hire a Virtual Bookkeeper

Scared about software on a remote server automatically handling your payroll? You might consider hiring a bookkeeper affordably through an online staffing website such as Upwork, and let a professional take care of things for you.

Going the virtual bookkeeper route has its own risks, to mitigate them, make sure to ask for references and do some online research on the bookkeeper’s background. Consider meeting via video chat to gauge whether the bookkeeper is trustworthy.

Virtual bookkeeper Linda Siniscal notes in LinkedIn that she builds trust with clients through her certification with the American Institute of Professional Bookkeepers. Certification means that Siniscal follows the association’s code of ethics, which call on bookkeepers to provide high-quality service, keep their clients’ information in confidence, always look out for their clients’ best interests, act with integrity, provide accurate information to government agencies and much more.

Cost: Starts at $20/hour.

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