10 Best Payroll and Accounting Software for Small Business in 2021

Small businesses, unlike large organizations, can’t hire a huge accounting team to manage every single penny. Small businesses already have limited resources at their hand, and most businesses can’t really afford to pay huge sums for an in-house accounting team. Best payroll and accounting software for small businesses can provide various benefits and improve efficiency. With good payroll software, a small business can have a clear understanding of its profitability, and keep a track of the accounting season.

When it comes to accounting software, best payroll and account software for small business are essential. When a business starts growing, its need for accounting becomes more complex and that’s where the best accounting software for small business comes in.

Fortunately, there’s no limit to affordable payroll software for small businesses. Each software offers various features at varying prices. To choose the best payroll and accounting software for small businesses, industry type and number of employees are two primary factors to focus on. The need for accounting software would be different for a freelancer and a small-scale business. Determining if the software is Good payroll software for small businesses is based on the needs of the firm.

To create our list of best payroll and accounting software for business, our team went through over 2 dozen best accounting software for small business. Here’s our pick for the 10 best payroll and account software for small businesses.

10 Best Payroll and Accounting Software

  1. QuickBooks Online – Best Overall

QuickBooks Online is one of the best payroll and accounting software for small business. Hundreds of thousands of professionals use QuickBooks Online for their account needs. One reason for that is because it offers endless online training resources and forums for user support.

The ease of use is also one plus point of the software, all the accounting features can be accessed from the main dashboard. QuickBooks Online is aimed at increasing the efficiency and fluidity of accounting processes.


  • Scalable 
  • Preferred by accounting professionals
  • Easy to integrate with other applications
  • Cloud-based for better data security
  • Also has a mobile app


  • Most users need to upgrade
  • Users can face occasional syncing errors with banks and credit cards
  1. Xero – Best for Micro-Business Owners

Xero is one of the best payroll and accounting software for small business and it is very simple. It has a very clean and intuitive interface that makes it incredibly easy to use.

That’s not all. With Xero, businesses can collect payment online from customers too, which makes it even more effective software.

Xero was founded in New Zealand in 2006, since then it has grown exponentially and has two million users globally. It offers 3 different plans and small businesses can choose the plan based on the needs of the firm. 


  • Cloud-based software for better data protection
  • Also has a mobile app
  • Payroll integration can be done with Gusto
  • Comes with a third-party app marketplace
  • Inventory management is simple


  • Limited reporting
  • A fee is charged for ACH payments
  • Customer service can be improved
  1. FreshBooks – Best for Service-Based Businesses

FreshBooks is considered one of the best payroll and accounting software for small business. It aims to solve one crucial accounting need for service-based businesses: invoicing. FreshBooks has a primary function to complete every possible activity related to invoices, also it can take care of a business’s common bookkeeping needs. Small businesses can send proposals and invoices, requests, deposits, receive payments, and track time on projects with ease. 

FreshBooks was founded in 2003 as just invoicing software. Businesses can choose from 4 plans, if you want a pocket friendly option, paying annually can help you avail 10% discount.


  • Cloud-based
  • Incredibly user-friendly interface
  • Super easy to integrate with third-party apps
  • One of the most affordable payroll software for small businesses
  • Advanced invoicing features


  • Can’t manage inventory
  • No available payroll service
  • The mobile app has some limitations
  1. Sage 50Cloud – Best for Inventory Tracking

Sage 50Cloud is a powerful small business desktop accounting application. What makes Sage50 best is its capability of combining financial tools and a wide array of customization options. Small businesses can integrate the software with Microsoft 365 and make it a hybrid solution. It can become a local, hard-drive-based software that can share data efficiently using the cloud. 


  • Sophisticated feature set
  • Easy to customize
  • In-depth contact and record of an item
  • Robust inventory management solutions
  • Scalable
  • Good customer support
  • Can be integrated with third-party apps


  • Can’t be used on any other operating system than Windows
  • Expensive compared to other software
  • No dashboard
  • The interface is kind of old
  • No mobile app
  1. Wave – Best Free Software

When it comes to affordable payroll software for small businesses, Wave comes out on top. It is the best payroll and accounting software for small business. However, it is only useful for businesses that only require simple invoicing solutions. For most freelancers and small service-based businesses, Wave’s free features will keep up with all the accounting needs. According to our team, it is one of the best free software. 


  • No limits on transactions and bills
  • Multiple account access by single user
  • Unlimited users
  • Has a robust mobile app full of features


  • Limited third-party app integrations
  • Has a higher fee on credit cards and ACH payments
  • Can’t manage inventory
  1. Zoho Books – Best for Mobile Access

Zoho Books is one of the best payroll and accounting software for small business. For cloud-based small businesses, Zoho Books is an excellent choice. It offers an exceptional user experience, comes at an attractive price, and offers various advanced tools. Some large-scale businesses can also use Zoho Books.


  • Affordable software
  • Excellent user interface and mobile app
  • Incredible depth in records and transaction forms
  • Multiple payment gateways support
  • Easy document management
  • Effective customer support


  • Projects have to be linked for time tracking
  • The integrated payroll feature is just limited to California, NYC, and Texas
  1. GoDaddy Bookkeeping – Best for Freelancers

If freelancers and entrepreneurs want an effective and comprehensive accounting solution then look no further than GoDaddy Bookkeeping. GoDaddy Bookkeeping can be integrated with Etsy, eBay, and Amazon. The software’s overall bookkeeping depth and flexibility are good, simple to use. However, it lacks some of the common functionality like some of its competitors. 


  • The software is really inexpensive
  • Effective invoicing tools and dashboard
  • Non-complicated time entries
  • Assists in calculating quarterly taxes
  • Can be integrated with Amazon, eBay, Etsy, and PayPal


  • Can’ track project or make bill payment
  • Minimal client information in records
  1. Sunrise – Best for Invoicing Tools and Double-Entry Accounting

Sunrise is another best payroll and accounting software for small business according to our team. The ease of use and features makes it one of the best options for freelancers and sole business owners. The software appeals to small businesses that require automation for double-entry accounting. It comes with time tracking, robust reports, and full mobile access. 


  • Brilliant user experience and clean dashboard
  • Best for double-entry accounting
  • Offers sales tax rulesets
  • Sales forms are handled well


  • Can’t track time or project
  • The mobile app is not as good as it should be
  • Minimal fields in contact and product records
  1. Kashoo – Best for Microbusinesses

What makes Kashoo one of the best payroll and accounting software for small business is income and expense management, support, and usability. The software is simple and fast and perfect for small businesses. Especially the businesses that don’t need to track inventory, and billing tools.


  • Simple and intuitive interface
  • Efficient income and expense management
  • Free email, chat, and phone customer support
  • Easy to integrate with SurePayroll


  • Few add-ons
  • No mobile app for android devices
  • Does not track time and project
  • It doesn’t have a standard dashboard
  1. Patriot Payroll – Best Payroll Software for Small Businesses

Last but not least is Patriot Payroll. Patriot Payroll has two different versions, and each version is perfect for small businesses. What makes Patriot Payroll even more effective is that its businesses can add two new services – HR and Tracking.

The basic version of the software comes at just $10 per month which is not too expensive for small businesses. 


  • Payroll setup and support
  • Flexible payment schedules
  • W-2 and W-3s filed for you


  • Doesn’t have a mobile app
  • Lacks some accounting features

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