Best Accounting Software for Medium-Sized Businesses

Compare the top accounting software for medium-sized firms and learn how to make the best choice for your business.

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With dozens of options available on the market, you may be wondering how to choose the right accounting system for your medium-sized business.

This guide will break down and compare the best accounting software for medium-sized businesses — detailing their features, pricing, pros and cons, so that you have all the information you need to make your best decision.

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QuickBooks Enterprise


  • Local only and with hosting plans available.

  • Advanced features and industry-specific tools.

  • Numerous integration options.

  • QuickBooks Payroll included with Gold, Platinum and Diamond plans.

  • Priority Circle customer support.


  • Expensive annual cost.

  • Pricing varies based on the number of users required.

  • Certain advanced modules (e.g. inventory and pricing) aren't included in the Gold and Silver plans.

  • Local-only versions are not compatible with Mac.

One of the most powerful accounting systems on the market, QuickBooks Enterprise is a great all-in-one solution for medium-sized businesses.

QuickBooks Enterprise offers industry-specific tools, reports and features for contractors, manufacturers and wholesalers, nonprofits and retailers. This robust software also includes advanced inventory features and advanced pricing options for your customers, meaning you can truly customize the software to fit your needs.

Additionally, QuickBooks Enterprise provides a built-in sales tax module to help keep you compliant with all sales tax laws that apply to your business. Plus, the three upper-level plans, Gold, Platinum and Diamond, offer QuickBooks Desktop Enhanced Payroll — allowing you to pay employees.

Example of QuickBooks Enterprise dashboard. Image source: QuickBooks

In terms of internal controls, QuickBooks Enterprise allows you to set custom user permissions for up to 40 users, meaning you have complete control over who sees what information in your growing medium-sized company.

This being said, however, the price of QuickBooks Enterprise will also vary based on the number of users you require. For the basic, Silver package with one user, this accounting software system will cost $1,340 per year. If you want the “with hosting” version of the same plan, you’ll pay more.

Of course, with the higher-level Gold, Platinum and Diamond packages, the cost will increase, but these plans also offer more.

With all of this in mind, it’s also worth noting that although QuickBooks Enterprise offers integrations and QuickBooks Payroll (with the higher-level plans), it does not necessarily provide the full range of payroll and HR capabilities you might need as a medium-sized business. Therefore, you might choose to outsource these functions or opt for a more specialized payroll and HR software that can integrate with QuickBooks Enterprise.

All in all, however, there’s no doubt that QuickBooks Enterprise is one of the best accounting systems for medium-sized businesses.

QuickBooks Online Advanced


  • Fully cloud-based; access wherever you have internet.

  • Includes 25 users and up to three accountants.

  • Features can be customized to your business; industry-specific tools.

  • Variety of integration options.

  • QuickBooks Priority Circle membership and support.


  • Doesn’t include payroll.

  • Monthly cost can be greater than certain versions of the more advanced QuickBooks Enterprise.

Although QuickBooks Online is typically considered one of the best accounting solutions for small businesses, the most advanced version of this software, aptly named QuickBooks Online Advanced, can be a great choice for medium-sized businesses.

With QuickBooks Online Advanced, medium-sized companies can experience the ease of use and mobility of QuickBooks Online, while also getting the robust accounting abilities they need. QuickBooks Online Advanced supports up to 25 users and three accountants, unlimited class and location tracking, unlimited chart of accounts entries, top-tier customer support and online training to help your team learn how to use the software.

Additionally, one of the most notable features of QuickBooks Online Advanced is that it includes a subscription to Fathom — a powerful reporting and analytics software. Fathom helps QuickBooks Online Advanced users get the most out of their accounting data by providing smart dashboards, the ability to customize projections and monthly KPI tracking.

Fathom reporting in QuickBooks Online Advanced. Image source: QuickBooks

Moreover, similarly to QuickBooks Enterprise, QuickBooks Online Advanced offers industry-specific tools — for professional service-businesses, legal companies, nonprofits, accountants, construction businesses and food and beverage companies.

Plus, everything in QuickBooks Online Advanced can be customized to your business and you can take advantage of the vast integration options in the QuickBooks app network.

This being said, QuickBooks Online Advanced costs $180 per month, putting it in line with certain versions of QuickBooks Enterprise in terms of pricing.

Overall, QuickBooks Online Advanced is one of the best cloud-based accounting software for medium-sized businesses — especially those who are looking for the flexibility and accessibility that QuickBooks Enterprise might be lacking.

Quickbooks Online

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on QuickBooks' website

Zoho Books


  • Affordable monthly pricing and discounts for annual subscriptions.

  • Seamless integration with other Zoho products (e.g. Zoho CRM, Inventory and Projects).

  • Cloud-based and user-friendly.


  • Restricts the number of contracts, workflows and users per plan — with a maximum of 10 users for the Professional plan.

  • No payroll services.

  • Features are not as advanced as some other solutions.

Although QuickBooks Enterprise and QuickBooks Online Advanced may be highly-regarded, they won’t be right for every business. Therefore, if you’re looking for a QuickBooks alternative, you might consider Zoho Books.

In comparison to the two QuickBooks products discussed above, Zoho Books isn’t quite as advanced — however, it is pretty all-inclusive, with a range of accounting features, numerous integration options and an affordable price.

With Zoho Books, you’ll have access to tools for invoicing, bill management, estimates, time and expense tracking, reporting, budgeting and more. In addition, all three of the Zoho Books plans include multi-currency and multilingual features, plus the Professional plan offers inventory tools, purchase orders, sales orders and up to 10 workflow rules per module.

Example of recurring bill management in Zoho Books. Image source: Zoho Books

Moreover, regardless of which of the three plans you choose, you’ll be able to integrate with the solutions in the vast Zoho product suite including Zoho CRM, Zoho Inventory, Zoho Expense, Zoho Subscriptions, Zoho Projects, Zoho Analytics and a variety of third-party tools.

This being said, although Zoho offers two lower-level plans, the Professional plan, for $29 per month or $290 per year, will be best suited for medium-sized businesses. It’s important to note, however, that Zoho does limit the number of users, contacts, workflow rules and custom views with each plan.

With all of this in mind, like QuickBooks Online Advanced, Zoho Books is one of the best cloud-based accounting software for medium-sized businesses — especially those are looking for a little more affordability and simplicity in their accounting solution.



  • Fully cloud-based, user-friendly and affordable software.

  • Unlimited users with all plans.

  • 700+ integrations in the Xero app marketplace.

  • Advanced features for expenses, project management and inventory.


  • Limited time tracking features.

  • Not as advanced as some enterprise-level software solutions.

  • Not as prevalent among accountants as QuickBooks is.

Similar to Zoho Books, Xero accounting is another worthwhile accounting software option for medium-sized businesses that are looking for a more affordable solution. Xero is also another top QuickBooks Online alternative — offering a robust feature set, over 700 integration options and significant flexibility.

With Xero, you’ll have three plan options, with the third one, Established, being the most suitable for medium-sized businesses.

The Established plan, at $60 per month, offers the ability to send unlimited invoices and quotes, enter bills, reconcile bank transactions and capture bills and receipts. In terms of advanced features, this version of Xero includes the Expenses module to capture and manage claims, as well as the Projects module, which allows you to track project time and costs.

Example of projects features in Xero accounting. Image source: Xero

In addition, Xero offers multi-currency accounting, inventory tools, purchase orders, asset management and more. Plus, although Xero doesn’t offer their own payroll services, they work with their partner, Gusto, to integrate the Gusto Payroll software with their accounting platform.

Moreover, and perhaps one of the most notable features of Xero is that they include an unlimited number of users, regardless of your plan — a feature that is pretty rare amongst small and medium-sized business accounting systems alike.

Therefore, again, similar to Zoho Books, Xero is one of the best cloud-based accounting software options for medium-sized businesses, as well as a top QuickBooks alternative. At only $60 per month, Xero will be more affordable than some other options, especially with unlimited users.

This being said, although Xero doesn’t offer the most advanced features on the market, it includes a vast range of accounting capabilities, plus an impressive number of integration options.

Sage 50cloud


  • Multiple plan options with advanced accounting features, including industry-specific tools.

  • Desktop solution with cloud storage and backup.

  • Integration with Microsoft Office and other Sage tools.

  • Monthly or discounted annual pricing.

  • Variety of customer support options and resources.


  • Limited users; additional users incur a higher price.

  • Limited third-party integration options.

  • Not as user-friendly as some solutions.

Another top accounting software for medium-sized businesses is Sage 50cloud. Among the vast Sage product suite, Sage 50 accounting is actually pretty similar to QuickBooks Desktop. This being said, despite the name, Sage50 is first and foremost a desktop-based accounting software, but it also offers cloud storage and backup.

With this in mind, Sage 50 accounting gives you the ability to manage a variety of accounting tasks — from basic billing and invoicing to advanced inventory, reporting, sales order management and more.

Sage 50cloud allows you to integrate with Microsoft Office 365, as well as other Sage tools, like Sage Payroll and Sage 50 CRM. Like QuickBooks Enterprise, there are three plan options for Sage 50, with the higher-level plans offering advanced features for job costing, budgeting, auditing and workflows.

Example of Sage 50cloud accounting software interface. Image source: Sage

The highest plan level, Sage 50cloud Quantum, offers up to 40 users, an unlimited number of companies and industry-specific features.

Sage50 is priced on a monthly or annual basis, with the initial plan option, Pro Accounting, costing $47.25 per month or $567 per year. It’s also important to note that with the higher-level plans, your price will vary based on the number of uses you require, once again similar to QuickBooks Enterprise. The more users you need, the higher the monthly or annual price.

All in all, however, Sage 50cloud is a very comparable alternative to QuickBooks Enterprise. In this way, it’s an ideal accounting system for medium-sized businesses that are looking for more advanced accounting tools, as well as a more traditional desktop-based solution.

To compare all the top picks side by side, see the table below

Accounting software


Key features

Best for

QuickBooks Enterprise

Starts at $1,340 per year for one-user desktop version

  • Plan options for local only and software with hosting.

  • Industry-specific tools and solutions.

  • Advanced inventory, pricing, reporting, and order management modules.

Medium-sized businesses looking for an all-in-one solution.

QuickBooks Online Advanced

$180 per month

  • Cloud-based software with access for 25 users.

  • Industry-specific tools and solutions.

  • Customizable roles, workflows, advanced reports, and more.

Fully cloud-based accounting software for medium-sized businesses.

Zoho Books

Starts at $15 per month for Standard Plan ($10 if billed annually)

  • Cloud-based software with mobile access.

  • Multi-currency and multi-lingual accounting.

  • Integration with other Zoho products (CRM, Inventory, Projects, etc.).

Medium-sized businesses looking for an affordable, yet well-rounded accounting software.


Starts at $12 per month for the Early plan

  • Cloud-based software with unlimited users.

  • Project and expense management modules with Established plan.

  • Over 700 third-party integration options.

Medium-sized businesses that need powerful and affordable accounting software, especially if they need several user accounts.

Sage 50cloud

Starts at $50.58 per month or $503.23 per year

  • Desktop-based software with cloud backup and storage.

  • Advanced inventory-, job costing-, budgeting, and auditing tools; industry-specific features as well.

  • Microsoft 365 integration, integration with other Sage products.

Medium-sized businesses that would prefer a more traditional desktop solution and are looking for advanced features.

Choosing the best accounting software for medium-sized businesses

First and foremost, you’ll want to ensure that any accounting software you’re considering is designed to accommodate a business of your size. You’ll want to adequately evaluate your needs to determine exactly what you’re looking for in your accounting solution. To this end, you might think about:

  • What specifically you want your accounting software to do and what kind of features you’re looking for.

  • What your monthly or annual budget is for this software.

  • Who will be using this platform and how many accounts you might need.

  • Will you want to integrate other business tools with this software, such as payroll-, HR- or inventory software.

  • Whether you prefer a local or fully-cloud based software.

Bookkeeping and accounting software

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on QuickBooks' website

QuickBooks Online $30 per month and up. Read Review.

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on FreshBooks' website

FreshBooks Accounting $15 per month and up. Read Review.

Sage 50cloud $47.25 per month (when paid annually) and up.

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Wave Financial Free (add-ons available).

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on Xero's website

Xero $12 per month and up.

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Zoho Books $0 per month and up.

A version of this article was first published on Fundera, a subsidiary of NerdWallet