5 Best Project Accounting Software

I evaluated each retail accounting system based on how well it supports real retail workflows, including inventory tracking, sales activity, and day-to-day financial management. I focused on what actually works in practice — how transactions flow, how inventory connects to accounting, and how easy it is to manage operations without extra tools.

• General features: I reviewed how each system handles core accounting tasks like general ledger, banking, accounts receivable, accounts payable, sales tax, and financial reporting. I gave more weight to platforms that deliver reliable, complete accounting without requiring workarounds.
• Retail-specific features: I examined tools that directly support retail operations, including inventory management, sales tax tracking, and POS integration. I prioritized systems that keep inventory and financial data aligned in real time.
• Pricing: I compared monthly costs, user limits, and feature availability across plans. I looked closely at whether key retail features are included in entry-level tiers or locked behind upgrades.
• Ease of use: I assessed how quickly a non-accountant can complete common tasks like invoicing, expense tracking, and reporting. I focused on navigation clarity and how much setup is required to get started.
• Customer support: I reviewed available support channels, including phone, chat, email, and help documentation, to see how easily users can get assistance when needed.
• User reviews: I analyzed average ratings from trusted review platforms to understand how each system performs in real-world use.

Zoho Books offers four subscription options with project accounting features.

• Professional: $50 per month for up to five users and unlimited invoices
• Premium: $70 per month for up to 10 users and unlimited invoices
• Elite: $150 per month for up to 10 users, unlimited invoices, and advanced inventory
• Ultimate: $275 per month for up to 15 users, unlimited invoices, and advanced inventory

Add-ons:

• Additional users: $3 per user, per month
• Receipt scanning: $10 for 50 scans per month
• Snail mail credits for sending invoices: $2 per credit

You can try any of Zoho Books’ paid plans for free for 14 days.

We selected Zoho Books as the overall best project-based accounting software for tracking project profitability because its Professional to Ultimate plans have all the project accounting features that you would expect to see. These include project creation, project estimations, assignment of project costs, allocation of inventory used, and project reporting. It also offers excellent general accounting features, including A/P and A/R management, banking and cash management, and income and expense tracking.

The biggest advantage of Zoho Books over other software listed in this guide is its excellent mobile accounting app. It has all of the features you’ll find in the desktop interface, including the ability to create and send invoices, accept payments, and record billable time. We believe these are crucial features for modern project managers and business owners who often work out of their offices.

Zoho Books stands out in almost all the categories in our rubric. It earned perfect marks for mobile accounting and integrations and did well in general accounting. It would also have aced project accounting if users could compare actual with estimated labor and inventory. If this feature is crucial to tracking your project profitability, then we recommend FreshBooks or Xero.

We are impressed with Zoho Books’ customer support because of the availability of phone support, but we docked a few points because it can be hard to find a local bookkeeper who is proficient in the program. It also took a hit in ease of use because it’s a very complicated program with many advanced features to master.

Only Xero’s Established plan offers project accounting features. It costs $80 per month for unlimited invoices and bills, plus multicurrency, receipt capture, and project tracking. You can access all of Xero’s features for free for 30 days.

We chose Xero as one of the best-based project accounting software because of its ability to accommodate unlimited users, making it ideal for companies with multiple accounting users. Other similar software, like FreshBooks and QuickBooks, include only one or a certain number of users in the base price and require an additional fee for each extra user.

Xero works well for project-based businesses because it can help you track time worked by your employees, bill clients for services performed, and generate project reports to track profitability. It also allows you to track COGS, making it suitable for businesses with inventory. It also has a fixed asset manager that keeps fixed asset records and calculates depreciation expenses automatically.

Unfortunately, similar to Zoho Books, the Xero Advisor network is a bit limited, so it can be difficult to look for a bookkeeper if you need help. If you want the ability to easily seek professional support, you will appreciate QuickBooks Online’s vast network of ProAdvisors.

Xero’s most impressive rating comes from its project management features. It’s slightly better than Zoho Books and QuickBooks Online because it allows you to compare actual and estimated labor and inventory. It also has other features, such as the ability to track billable time and COGS.

A slight drawback is that it doesn’t have a built-in feature for storing and managing project documents. You may consider integrating it with external software like Hubdoc or explore an alternative like Zoho Books, which has a dedicated document management tool.

Another shortcoming is customer support—it doesn’t offer live customer service, like phone support and live chat. If you want access to excellent customer support, you should consider Zoho Books or FreshBooks.

QuickBooks Online has two tiers that will enable you to track costs by project.

• Plus: $99 per month for up to five users
• Advanced: $235 per month for up to 25 users

You can either sign up for a 30-day free trial or purchase right away to get 50% off for three months.

QuickBooks Online is widely used by many businesses because of its powerful accounting features. While it has no industry-specific features, it can be customized to nearly any type of business. Most project-based businesses will find QuickBooks Online more than enough, as it includes essential project management features, like the ability to create and track projects, track time, and bill clients for work performed.

One of its advantages is that it gives you access to a large support network of QuickBooks ProAdvisors. It provides a “Find-a-ProAdvisor” directory on its website, where businesses using QuickBooks Online can search for and connect with ProAdvisors who specialize in project accounting or another specific area of expertise. It also excels in project accounting, with features such as time tracking, milestone-based billing, and progress invoicing serving as useful tools.

On the flip side, QuickBooks Online is a bit expensive, especially since you have to purchase at least the Plus plan at $99 monthly to use project accounting. If you want a more affordable solution, you should consider Zoho Books, which tops our list of the best QuickBooks Online alternatives.

QuickBooks Online aced the integration category and earned excellent scores in general accounting and project management, which isn’t surprising given that it’s our overall best small business accounting software. However, we would like to see QuickBooks add a dedicated document management for storing and managing project documents, like blueprints, contracts, and permits. The provider may draw inspiration from Zoho Books, which has a designated inbox for receiving financial files like receipts and invoices.

Further, QuickBooks Online didn’t do well in pricing as it’s a bit expensive, and the Plus plan supports only up to five users. It also fell short in our mobile app category, as there are some missing features, such as the ability to enter bills and record time worked; Zoho Books is the only provider listed here to have aced our mobile app evaluation.

We could have awarded QuickBooks Online a higher mark for customer support if you didn’t have to upgrade to Advanced to be able to contact phone support directly. Other software like Zoho Books and Sage 50 offer phone support in all their plans.

FreshBooks offers two tiers that include project management features:

• Premium: $65 per month, unlimited billable clients
• Select: Custom pricing for unlimited billable clients and specialized features

Add-ons:

• Additional team members: $11 per person, per month in all plans
• Advanced payments: $20 per month

We selected FreshBooks as the best accounting software for service-based businesses because of its robust project management features, such as the ability to track billable time and convert time entries to invoices. It is ideal for small businesses that bill clients based on the time worked by their employees, and one of its most useful features is the ability to compare estimated and actual project costs, which is impossible with Zoho Books.

A huge drawback to using FreshBooks is that it lacks inventory management features. If inventory is an important part of your business, you should consider QuickBooks Online or Xero.

FreshBooks did a great job in terms of project accounting and integrations, but it took a hit in general accounting because of the lack of inventory management features and the odd way in which it handles banking transactions. FreshBooks requires the user to establish a live bank feed to sort payments into various payment accounts. Other software allow bank feeds, but FreshBooks is the only one we’ve seen that requires it.

It also lost points for customer service because it doesn’t provide live chat support, and the online user community isn’t that big. Also, it’s not as easy to use as we expected because the onboarding wizard isn’t that intuitive.

Additionally, we deducted points for pricing because it can be costly for businesses needing more than a couple of users. We also wanted the mobile app to improve by adding new features, like the ability to enter and pay bills and track billable time on the go—things Zoho Books’ powerful mobile app can do.

Sage 50 Accounting is available in three subscription options, all of which support project accounting:

• Pro Accounting: $60.08 per month; one user only
• Premium Accounting: From $103.92 per month for one user to $293.17 per month for five users; up to five users only
• Quantum Accounting: From $177.17 per month for one user to $452.67 per month for 10 users; custom priced for over 10 users

If you need payroll, then you can bundle your package with a payroll subscription with prices starting at $768.75 per year for one to 10 employees.<

As a locally installed software, Sage 50 Accounting is ideal for companies that operate in remote areas with unreliable or no internet access. You just need to install it on a local computer, and you can work with it without interruptions. Desktop software also allows faster data entry than cloud-based software since you don’t have to wait for the screen to refresh after each entry. There are other desktop accounting software, but Sage 50 Accounting provides a more affordable solution without compromising on essential project accounting features.

It has excellent project tracking features that allow you to track the progress of each project you manage, from creating initial quotes to billing your customers. If you charge clients on an hourly basis, you can integrate it with time tracking tools, like Sage Timeslips and Journyx. To help you better track profitability, Sage 50 Accounting has advanced job costing tools that let you monitor various expenses, including labor, materials, and overheads.

Another thing we like about Sage 50 Accounting is that it allows you to manage multiple companies, and you can even generate consolidated reports for those companies. This feature is essential for companies that manage large-scale projects across different locations. Furthermore, despite being desktop software, all Sage 50 Accounting subscriptions come with Remote Data Access, a service that allows you to access your software and access your data remotely.

On the downside, Sage 50 Accounting is complicated to navigate without prior experience. Also, it is not that popular in the US and has relatively few bookkeepers specializing in it, so it might be difficult to seek support. If you want an easier-to-use software with easy access to bookkeeping support, QuickBooks Online is a great alternative.

Sage 50 Accounting earned a perfect mark for integrations and excelled in both general and project accounting. It would have aced project accounting if users could integrate it with project management tools to enable additional features like task scheduling and collaboration tools. It scored zero for mobile accounting because the app can only capture expense receipts—nothing else.

Meanwhile, we gave it a below-average score for pricing because each additional user costs extra. In some software, like QuickBooks Online, each plan supports a certain number of seats, while other solutions, like Xero, even allow unlimited users. Sage 50 Accounting did well in customer support, but it fell short in ease of use because of its outdated user interface.