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12 Best Payroll Software for Bookkeepers in 2019

Category: B2B News
What is the best payroll software for bookkeepers?
The best payroll software for bookkeepers is QuickBooks Pro,  a cloud-based/on-premise software that offers both self-service and full-service payroll. It makes the entire payroll process easy, accurate, and fast with a simple user interface for direct payments and robust tax compliance tools, among others.

Bookkeeping can make or break your business. Maintaining a sound bookkeeping practice is essential in keeping a business confidently afloat. The growth and stability of businesses quietly rest on the backs of bookkeepers and they need all the help they can get. Rightly so, bookkeepers must be fully equipped when it comes to payroll software they use.

Today’s payroll software market is booming with more and more businesses opting to outsource their payroll needs.  It can be confusing though, some are providers offering both software and service, while others are vendors peddling the software component alone. Still, others let you scale to full HR software with integrated accounting tools.

To navigate the overwhelming market, we’ve come up with the list of the 12 best payroll software for bookkeepers to help you gauge the definitive tools currently offered in the market. Ultimately, you will be able to determine which software is best for you and your bookkeeping needs.

best payroll software for bookkeepers

Historical records of bookkeeping can be traced to as early as 2600 BCE with bookkeeping serving as a definitive mark of a civilized and advanced society. We’ve come a long way, for sure, from simply reconciling records of the in and out of goods and services.

Yet companies still struggle with the usual bookkeeping challenges: tracking cash flow, unforeseen expenses, and impact of disasters, among others. Managing payroll still presents the usual challenges: meeting federal and local regulations and reconciling payroll expenses with finances. Traditionally, one of the strategic ways to address cumbersome bookkeeping problems is to outsource key accounting tasks.

Percent of companies that outsource these accounting services


Tax preparation






Tax planning


Personal finances



Source: Wasp Barcode Technologies survey

Designed by

However, outsourcing isn’t the only game in town. Today’s payroll software, accounting solutions and HR software solutions are more than capable of addressing payroll processing issues, driven by these trends:

  1. Big Data Analytics. The advent of technology that allowed for quick analysis of huge chunks of data gave rise to this development.
  2. Cloud Accounting. It provides cost efficiency and on-the-go access 24/7.
  3. Automation. Makes entries more accurate and faster to reconcile.
  4. Collaborative Bookkeeping. It helps businesses with remote units to consolidate their books.
  5. Outsourcing. Delegation of non-core tasks are fast becoming the norm given its cost-efficiency

In this list, we evaluated different payroll solutions based on their ability to address the issues above and their capability driven by the trends we cited. Our best payroll solutions here are expected to delight bookkeepers looking to lend to their payroll more efficiency and accuracy.

12 Best Payroll Software for Bookkeepers

1. QuickBooks Pro

QuickBooks dashboard example

QuickBooks Pro tops our list of the best payroll software for bookkeepers for its rich feature set and cloud/on-premise flexibility. It provides automation, analytics, and compliance tools to its users. In addition, it gives its users the option to choose between a manual self-service plan or a fully automated service plan. It also gives bookkeepers the option for more customization and personalization of payroll tools.

Furthermore, it’s a top favorite among bookkeepers as it has an outstandingly simple user interface that streamlines bookkeeping processes and speeds up payroll transactions.

You can give its features and tools a try when you sign up for QuickBooks Pro free trial here.

QuickBooks Pro boasts that it can run payroll in just five minutes. Likewise, its tools were designed to answer to such needs with features that allow for a one-day payment transfer, calculated paychecks, direct deposits, and real-time tracking for the payment of both employees and contractors. In addition, all its users have access to unlimited payrolls.

Bookkeepers will also appreciate how QuickBooks Pro has built-in tax tools that make compliance easy. Printable W-2 forms are accessible together with payroll tax tools that fully comply with US tax laws. Moreover, QuickBooks Pro offers a no-penalty guarantee to all its users. This guarantee is possible through a dedicated in-house pool of experts that QuickBooks Pro assigns to each of its users. Hence, bookkeepers will really feel that they have extra hands helping them.

QuickBooks Pro is compatible with all Intuit products. It has an open API that enables integration to any third-party apps. It’s available for as low as $18/month with an additional $4/month per employee.

2. OnPay

OnPay dashboard example

OnPay makes payroll easy and hassle-free. It offers full-service payroll and comprehensive tools in granting benefits and assessing HR laws in 50 states. It easily nabs the second spot for it allows bookkeepers to easily monitor a streamlined payroll process that covers even taxes. In addition, bookkeepers will enjoy OnPay tools that allow for automated tax payments and periodical filings.

What makes it stand out among other payroll software is its ability to cater to bookkeepers’ varying needs when it comes to fulfilling different payroll needs per state. It gives bookkeepers the confidence and security to take on daily tasks without being limited by unique laws and mandates that each state requires. Bookkeepers will not be stalled if they use OnPay for they can take on tasks smoothly regardless of particular demands.

Should you want to investigate the platform firsthand, you can easily do so when you can sign up for OnPay free trial here.

Payroll is a particularly tricky arena that demands accuracy lest discrepancies arise resulting in legal dilemmas and headaches. OnPay removes this concern for bookkeepers by providing features that process W-2 and 1099 forms together with 401(k) Plans, PTO accruals, and health benefits. Bookkeepers can rest easy that everything that needs to be complied with is properly evaluated and completed.

In addition, OnPay integrates with top accounting software like QuickBooks Online, QuickBooks Desktop, Xero, and FreshBooks. For convenient time tracking, it integrates with When I Work, Humanity, TSheets, and Deputy. OnPay is available in the market for as low as $36/month with an additional $4/month per employee.

3. Gusto

Gusto dashboard example

Gusto is a solid software with intuitive payroll tools that can swiftly organize payroll tasks and processes. It simplifies payroll with its clean and direct user interphase. Bookkeepers will find themselves enjoying how fast it completes payroll processes. Bookkeepers will also appreciate how the software did not use technical terminologies. All tools and features are labeled in simple English.

Moreover, it streamlines tasks that often overwhelm bookkeepers with its one-click compliance checker and reports. In addition, it has straightforward tools for payroll that has special categories and settings for contractors, time offs, and benefits. It also organizes referrals and documents. It also has a secured admin protocol that ascertains the protection, confidentiality, and fidelity of business files.

The vendor offers a comprehensive free trial to get you up to speed with the features. You can sign up for Gusto free trial here.

Gusto integrates with third-party apps like BambooHR, QuickBooks, Xero, When I Work, and Kin. Gusto is available in the market for $39/month with an additional $6/month per employee.

4. Sage 50cloud

Sage 50 dashboard example

Sage 50cloud is best for bookkeeping needs of sole traders, start-ups, and small businesses. It has sleek tools for inventory, invoicing, budgeting, taxes, and cash flow management. In addition, bookkeepers will enjoy how they have the option to choose between desktop or cloud-based tools.

Sage 50cloud is recommended for bookkeepers for its tools that can easily reconcile bank statements with multiple accounts accurately. Moreover, it has tools that allow for automatic calculation and submission of GST returns. These tools come in handy for bookkeepers who want to complete payroll processes instantly with zero error and discrepancies.

You can easily sign up for Sage 50cloud free trial here and get to know the features firsthand at no cost and without commitment.

Sage 50cloud integrates with third-party apps like BQE Core, QCommission, Realtrac, and Skype. It’s available in the market for $44.97/month.

5. ADP Workforce Now

ADP Workforce dashboard example

ADP Workforce Now is a scalable payroll software that bookkeepers will favor with its tools that offer solutions for employee needs every step of the way — from recruitment to retirement, all legally mandated benefits are accounted for.

It has payroll and time and attendance tools that allow bookkeepers to instantly prepare accurate reports. Should bookkeepers be busy with particular projects, ADP Workforce Now even offers an in-app feature that allows for the easy outsourcing of payroll and HR tasks.

Pricing for ADP Workforce Now is determined by quote.

6. Xero

Xero dashboard example

Xero is a favorite among accountants for its real-time tools that allow for live cash flow monitoring. Its tools allow bookkeepers to log in anytime regardless of their location around the globe. The app is online and can be accessed by PC, Mac, phone, or tablet. It’s ideal for small businesses as it offers competitive price points that allow users to purchase its services for as low as $9/month.

There are two main reasons why Xero is one of the best payroll software for bookkeepers: mobility and speed. Xero offers optimum mobility via its mobile app that allows bookkeepers to track expenses, send invoices, and reconcile records anywhere in just a click. Xero is also known for its robust integration tools that allow for more than 400 third-party apps like Stripe, Evernote, Harvest, PayPal, and Bill to seamlessly work with its native tools and features.

7. Dayforce HCM

Dayforce HCM dashboard example

Dayforce HCM is a transformative software that’s ideal for bookkeepers who want to focus on employee records and needs. It’s a web-based payroll app that primarily focuses on workforce management, document management, payroll, benefits, tax, HR management, and analytics.

Dayforce HCM has its edge when it comes to providing tools that improve the engagement and participation of employees in the bookkeeping process. With its tools that actively engage employees, bookkeepers can easily assess if hires are developing and delivering in such a manner that deserves rewards.

In addition, it has a real-time payroll that continuously calculates and updates payroll records with robust audit tools. Bookkeepers can also utilize its reports and analytics to come up with data-supported informed decisions in an instant.

Pricing for Dayforce HCM is determined by quote.

8. Wave

Wave dashboard example

Wave is a free payroll software that allows bookkeepers to track expenses, send an invoice, and organize receipts at absolutely no cost. It can easily simplify the bookkeeping needs of startups and small businesses.

Wave offers robust bookkeeping tools for small businesses. Bookkeepers who are just beginning to understand how cash flow and expense tracking actually takes place in an organic business ecosystem will find Wave handy as it simplifies all the necessary bookkeeping transactions, tools, and processes. It’s absolutely free but it offers premium payroll tools for its paid users.

9. Zenefits

Zenefits dashboard example

Zenefits is the ideal software for bookkeepers with particular needs and demands. Apart from its main tools that allow for the streamlining of payroll, compliance, and HR management, it also provides its users with personalized tools. Zenefits incorporates a workflow framework that integrates its multiple tools making it ideal for startups and SMBS who are just beginning to build a solid financial ecosystem.

Zenefits has a comprehensive set of tools for organized and manageable monitoring of employee benefits. It has expanded features that cater to medical benefits, dental benefits, vision benefits, life benefits, disability benefits, loans, savings, and even commuter benefits. This expanded feature makes it ideal for bookkeepers looking for more specialized software that can handle complex needs for the provision of benefits.

Zenefits integrates with numerous third-party apps like Slack, Lever, Office365, Zugata, and Salesforce. It’s available in the market for as low as $5/month per employee with a monthly base fee of $40.00.

10. Intuit Payroll

Intuit Payroll dashboard example

Intuit Payroll is a payroll software ideal for bookkeepers who want a significantly faster payroll process. It offers tools that allow for a 24-hour direct deposit with unlimited payroll runs that speeds up the distribution of paychecks. It even has a Same-Day Direct Deposit tool that makes bookkeeping easy and less complicated.

Intuit Payroll boasts of an automated payroll system that can complete consolidating employee records in just five minutes. In addition, it also has a service that offers free W-2s. This service is particularly unique as Intuit Payroll takes on the filing process and sends W-2s on your behalf. Bookkeepers who want to rest easy when it comes to handling and organizing W-2s can relax if they’d opt to use Intuit Payroll.

Intuit Payroll integrates with QuickBooks and QuickBooks Online. It’s available for as low as $17.50/month with an additional $4/month per employee.

11. Namely

Namely dashboard example

Namely is an ideal payroll software for bookkeepers who want expanded tools when it comes to tracking attendance, monitoring cash flow, and complying with benefits. It can handle the bookkeeping needs of startups, SMBs, and enterprises.

Namely stands out when it comes to its personalized features with expanded tools that make bookkeeping easy. It has a mobile app that engages employees and allows bookkeepers to verify attendance, employee profiles, and budget records in an instant.  In addition, it has advanced security tools that provide access and permission on a role-based basis. It also allows for eSignatures and the incorporation of org charts.

Namely also has expanded tools for employee profiles that accelerates the tracking and monitoring of employee salary, benefits, attendance, and leaves. Namely integrates with numerous third-party apps like NetSuite, Jazz, Radius, and TSheet.

Pricing for Namely is determined by quote.

12. Sage HRMS

Sage HRMS dashboard example

Sage HRMS is an HR-centric payroll software that fits bookkeepers with proactive tasks in monitoring employee development and growth. It offers reports and analytics that seamlessly integrate tracking tools. The software is ideal for medium businesses and large enterprises.

The employee tracking tool is fully customizable. This function makes strategic planning easier for bookkeepers with a grounding that’s rooted in the concept of Return On Employee Investment. Be it the management of payroll, benefits, recruitment, or attendance, all data are pooled and analyzed to create full employee performance regularly. This tool makes it easier for bookkeepers to see the growth trajectory and mitigate risks. Sage HRMS also offers paperless HR management making it ideal for bookkeepers who prefer a full-on digital experience.

Sage integrates with multiple third-party apps like CompuPay, LightWork, and iRecruit. It’s pricing is available by quote.

7 Things to Consider When Choosing Payroll Software

To come up with the best payroll software for bookkeepers, it’s important to consider and evaluate if the following important factors are present:

  1. Automation. Opting to automate tasks will significantly speed up payroll transactions and increase overall bookkeeping productivity.
  2. Analytics. The proper utilization of big data can boost a company’s development and result in increased profits. In some instances, you may want to check if the payroll app integrates with leading business intelligence software for small companies to help you analyze disparate data.
  3. User Interface. Payroll is taxing in itself so it’s best for bookkeepers to opt for software with simple, clean, and easily understandable commands that can be accessed in a click through the dashboard.
  4. Compliance. To prevent legal concerns, it’s important to opt for payroll software that can comprehensively provide guideposts, scheduling, and timely notifications when it comes to accomplishing governmental requirements for employees’ income tax and benefits.
  5. Benefits Management. Providing sound benefits is essential in keeping employees happy, content, and attended to. Incorporating benefits expenditure is essential in maintaining proper expenditure hygiene.
  6. Time tracking. In-app time tracking tools make payroll processing and data verification hassle-free. A payroll app may also integrate with third-party time-tracking software, which in itself isn’t a bad thing.
  7. Compensation Management. This tool is the backbone of every payroll software and it’s a must that features are placed to secure an error-free and accurate compensation scheme.

All these should be possible in your payroll software of choice. If you want to start off on the right foot, why not try QuickBooks Pro? It is capable of the features above either natively or via integration. You can also use it as a benchmark at no cost to see how other solutions measure up. You can easily sign up for QuickBooks Pro free trial here.

If you are a payroll service provider though, you might need more advanced features than what a freelance bookkeeper requires. You can investigate more options in our 20 best payroll software for payroll service providers guide.

By Jenny Chang

Senior writer at FinancesOnline who writes about a wide range of SaaS and B2B products, including trends and issues on e-commerce, accounting and customer service software. She’s also covered a wide range of topics in business, science, and technology for websites in the U.S., Australia and Singapore, keeping tabs on edge tech like 3D printed health monitoring tattoos and SpaceX’s exploration plans.

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