12 Best Payroll Software for Bookkeepers in 2024

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.

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.

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 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.

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 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 an OnPay free trial plan.

OnPay

Try out OnPay with their free trial

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. Rippling

Rippling is designed as an all-in-one HR and IT system for small and mid-sized businesses. The platform offers a robust payroll management module that automatically syncs with your HR data to calculate salaries, allocate benefits, as well as deduct 401ks and taxes. With this platform, users can run payroll within a few minutes and with minimal error. After which, users can then generate custom reports to get an idea of compensation trends as well as ensure that all employees are properly compensated.

A great thing about this platform is that it is not limited to payroll processing. As a complete HR software, it has a unified employee database and also offers functionalities for onboarding, task management, position management, and approval automation. Rippling also comes with an electronic document management system that supports online signatures for a completely paperless HR and payroll process. This also makes it ideal for bookkeepers who prefer a full-on digital experience.

The vendor offers a free demo should you be interested in learning more about the functionalities of the platform. Just make sure to get in touch with their representatives.

As for pricing, Rippling offers a quote-based plan that starts at $8/user/month. The vendor will provide you with a custom subscription price after assessing the unique requirements of your company.

4. Gusto

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 a Gusto free trial.

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.

5. Sage 50cloud Accounts

Sage 50cloud Accounts is an online accounting software providing small and midsized businesses with features, such as inventory, taxes, cash flow, budgeting, and invoicing. It also offers a broad selection of add-ons for payroll, credit card processing, and more. Businesses can use this tool’s built-in accounting best practices to remain compliant and monitor their finances. Users can bill customers and make payments on-the-go with it. For accountants, they can gain real-time access to accounting books.

Sage 50cloud Accounts is a hybrid as it is a desktop system that has a cloud element for data storage and access. It can track purchases and vendors and settle payments too. It also comes with expense management functionalities that include bank feeds and mobile payments. In addition, it can connect to bank accounts and give access to financial reports from any online device.

Sage 50cloud Accounts integrates with Microsoft tools, like MS Office 365. It’s available in the market for a starting price of $50.58/month.

6. ADP Workforce Now

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.

7. Xero

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.

8. Dayforce HCM

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.

9. Wave

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.

10. Zenefits

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.

11. Intuit Payroll

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.

12. Namely

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.

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.

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.

Key Insights

• QuickBooks Pro:
  • Offers both self-service and full-service payroll options
  • Simple user interface with direct payments and robust tax compliance tools
  • Provides automation, analytics, and compliance tools
  • Offers a no-penalty guarantee through dedicated in-house experts
  • Compatible with all Intuit products and integrates with third-party apps
• OnPay:
  • Full-service payroll with comprehensive HR law compliance tools for all 50 states
  • Automated tax payments and periodical filings
  • Integrates with top accounting and time-tracking software
• Rippling:
  • All-in-one HR and IT system for small and mid-sized businesses
  • Payroll module syncs with HR data for seamless calculations and reports
  • Includes functionalities for onboarding, task management, and document management
• Gusto:
  • Intuitive payroll tools with a simple user interface
  • One-click compliance checker and reports
  • Integrates with third-party apps like BambooHR and QuickBooks
• Sage 50cloud Accounts:
  • Online accounting software with features like inventory, taxes, and cash flow management
  • Hybrid system with cloud storage and access
  • Integrates with Microsoft Office 365
• ADP Workforce Now:
  • Scalable payroll software with solutions for employee needs from recruitment to retirement
  • Offers in-app feature for outsourcing payroll and HR tasks
• Xero:
  • Real-time tools for live cash flow monitoring
  • Offers optimum mobility via a mobile app
  • Integrates with over 400 third-party apps
• Dayforce HCM:
  • Web-based payroll app focusing on workforce management and employee engagement
  • Real-time payroll with robust audit tools
• Wave:
  • Free payroll software ideal for startups and small businesses
  • Offers premium payroll tools for paid users
• Zenefits:
  • Streamlines payroll, compliance, and HR management with personalized tools
  • Integrates with numerous third-party apps
• Intuit Payroll:
  • Automated payroll system with 24-hour direct deposit and unlimited payroll runs
  • Integrates with QuickBooks
• Namely:
  • Expanded tools for tracking attendance, monitoring cash flow, and complying with benefits
  • Personalized features with a mobile app for employee engagement

FAQ

1. What makes QuickBooks Pro a top choice for bookkeepers? QuickBooks Pro offers both self-service and full-service payroll options with a simple user interface, robust tax compliance tools, automation, analytics, and a no-penalty guarantee through dedicated in-house experts. It also integrates with all Intuit products and third-party apps.
2. How does OnPay handle payroll compliance across different states? OnPay offers comprehensive tools for full-service payroll and HR law compliance across all 50 states, including automated tax payments and periodical filings. It integrates with top accounting and time-tracking software to streamline the payroll process.
3. What additional features does Rippling offer besides payroll management? Rippling provides an all-in-one HR and IT system, including functionalities for onboarding, task management, position management, and document management. It supports online signatures and offers a fully digital HR and payroll process.
4. Why is Gusto considered user-friendly for bookkeepers? Gusto simplifies payroll with an intuitive user interface and straightforward tools, including a one-click compliance checker and reports. It avoids technical jargon and integrates with third-party apps for added convenience.
5. What are the key functionalities of Sage 50cloud Accounts? Sage 50cloud Accounts offers features such as inventory, taxes, cash flow, budgeting, and invoicing, along with add-ons for payroll and credit card processing. It is a hybrid system with cloud storage and integrates with Microsoft Office 365.
6. How does ADP Workforce Now support bookkeepers in managing payroll? ADP Workforce Now provides scalable tools for payroll and time and attendance, offering accurate report preparation and in-app outsourcing of payroll and HR tasks. It supports employee needs from recruitment to retirement.
7. What advantages does Xero offer for mobile bookkeeping? Xero provides real-time tools for live cash flow monitoring and can be accessed via PC, Mac, phone, or tablet. It integrates with over 400 third-party apps and offers robust integration tools for seamless bookkeeping.
8. What employee engagement tools are available in Dayforce HCM? Dayforce HCM focuses on workforce management and employee engagement, offering tools that improve employee participation in the bookkeeping process. It provides real-time payroll updates and robust audit tools.
9. Is Wave a suitable payroll solution for startups? Yes, Wave is a free payroll software ideal for startups and small businesses. It simplifies bookkeeping transactions and offers premium payroll tools for paid users.
10. How does Zenefits cater to specific bookkeeping needs? Zenefits offers personalized tools for payroll, compliance, and HR management, incorporating a workflow framework that integrates multiple tools. It provides comprehensive benefits management and integrates with numerous third-party apps.
11. What makes Intuit Payroll efficient for payroll processing? Intuit Payroll offers an automated system with 24-hour direct deposit and unlimited payroll runs, speeding up the distribution of paychecks. It also handles the filing and organization of W-2s and integrates with QuickBooks.
12. What personalized features does Namely provide for bookkeepers? Namely offers expanded tools for tracking attendance, monitoring cash flow, and complying with benefits. It has a mobile app for employee engagement and advanced security tools for role-based access and eSignatures.