FreshBooks vs. QuickBooks Desktop Enterprise

Overview
ProductRatingMost Used ByProduct SummaryStarting Price
FreshBooks
Score 8.7 out of 10
Small Businesses (1-50 employees)
FreshBooks is an accounting service for small businesses. The solution enables users to send and manage invoices, track billable time and collect online payments. The vendor’s value proposition this that their solution provides a straightforward service that simplifies the billing process.
$21
per month
QuickBooks Desktop Enterprise
Score 8.0 out of 10
N/A
QuickBooks Desktop Enterprise is a widely-used accounting package designed for small to mid-sized businesses. It is the top of the QuickBooks line. Pricing starts at $3,000 for five users, and goes up depending on the number of additional users. They also offer an Advanced Inventory module for $999 / year.
$1,703
per year per user
Pricing
FreshBooksQuickBooks Desktop Enterprise
Editions & Modules
Lite
$21
per month
Plus
$38
per month
Premium
$65
per month
Select
Custom Pricing
Diamond
$447
per month per user
Diamond with Remote Access
$513
per month per user
Gold
2,210.00
per year per user
Platinum
2,717.00
per year per user
Gold with Remote Access
3,000.00
per year per user
Platinum with Remote Access
3,504.00
per year per user
Offerings
Pricing Offerings
FreshBooksQuickBooks Desktop Enterprise
Free Trial
YesNo
Free/Freemium Version
YesNo
Premium Consulting/Integration Services
NoNo
Entry-level Setup FeeNo setup feeNo setup fee
Additional Details10% discount for annual pricing.
More Pricing Information
Community Pulse
FreshBooksQuickBooks Desktop Enterprise
Considered Both Products
FreshBooks
Chose FreshBooks
It was not my choice to select FreshBooks, but my client finds it easier to do billing with FreshBooks over QuickBooks.
QuickBooks Desktop Enterprise
Chose QuickBooks Desktop Enterprise
By comparing all these 3 tools. Quick Books approach is more intuitive, educative, lot of insights about yearly/quarterly state-wise changes, may it be forms, etc. while others are like they take a long time to release updates. QuickBooks support team and the tool knowledge …
Chose QuickBooks Desktop Enterprise
QuickBooks seems to be more focused on the accounting side of the business than FreshBooks. I've also tried Peachtree software. Peachtree seemed more restrictive. The user had to adapt their procedures to the methods of the software rather than the reverse. I tried …
Chose QuickBooks Desktop Enterprise
All competitors do invoice and a/p. Many of the listed competitors do better asset tracking and inventory. The larger packages get too complex too quickly and become an administrative burden as well as an implementation burden. QuickBooks is easier to set up the COA and …
Chose QuickBooks Desktop Enterprise
Significantly better in every way except having a cloud access system that does not require a hosting service.
Chose QuickBooks Desktop Enterprise
This is a long list, and every program has it's pros and cons. Ultimately we chose Quickbooks because of simplicity, 3rd party integrations, and cost.
Chose QuickBooks Desktop Enterprise
Ultimately, the decision really came down to the advisor that we chose to use. Pricing was also a big factor and the ability to tie into other applications/programs.
Chose QuickBooks Desktop Enterprise
Bill.com - Because it is the specialised AP Management portal that comes with approval and payment workflow in itself and syncs with QB. Expensify - Because it is the intelligent Expense reimbursement tool that QuickBooks Desktop doesn't offer.
Chose QuickBooks Desktop Enterprise
Quickbooks Enterprise is the best overall software for the average business which has outgrown small business accounting software. It only fails in small areas for companies in unique areas of business like fabrication shops, job shops, or custom creators making one of a kind …
Features
FreshBooksQuickBooks Desktop Enterprise
Customization
Comparison of Customization features of Product A and Product B
FreshBooks
9.1
35 Ratings
16% above category average
QuickBooks Desktop Enterprise
7.4
85 Ratings
4% below category average
API for custom integration9.330 Ratings7.768 Ratings
Plug-ins8.926 Ratings7.177 Ratings
Security
Comparison of Security features of Product A and Product B
FreshBooks
10.0
41 Ratings
20% above category average
QuickBooks Desktop Enterprise
8.7
178 Ratings
6% above category average
Single sign-on capability10.01 Ratings9.1139 Ratings
Role-based user permissions9.941 Ratings8.4176 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
FreshBooks
7.5
57 Ratings
4% below category average
QuickBooks Desktop Enterprise
8.3
197 Ratings
6% above category average
Dashboards8.957 Ratings8.2167 Ratings
Standard reports8.755 Ratings8.9195 Ratings
Custom reports4.82 Ratings7.7187 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
FreshBooks
7.5
56 Ratings
2% below category average
QuickBooks Desktop Enterprise
7.9
201 Ratings
4% above category average
Accounts payable8.041 Ratings8.7194 Ratings
Accounts receivable9.455 Ratings8.4194 Ratings
Cash management7.03 Ratings8.9177 Ratings
Bank reconciliation7.02 Ratings9.4190 Ratings
Expense management6.651 Ratings8.1178 Ratings
Time tracking7.642 Ratings6.692 Ratings
Multi-currency support7.01 Ratings6.865 Ratings
Regulations compliance6.021 Ratings7.477 Ratings
Self-service portal9.13 Ratings7.079 Ratings
Fixed asset management00 Ratings7.2135 Ratings
Multi-division support00 Ratings7.4107 Ratings
Electronic tax filing00 Ratings7.3100 Ratings
Global Financial Support00 Ratings6.138 Ratings
Primary and Secondary Ledgers00 Ratings8.472 Ratings
Intercompany Accounting00 Ratings7.795 Ratings
Localizations00 Ratings8.354 Ratings
Journals and Reconciliations00 Ratings9.3150 Ratings
Enterprise Accounting00 Ratings8.6100 Ratings
Configurable Accounting00 Ratings8.598 Ratings
Centralized Rules Framework00 Ratings8.461 Ratings
Standardized Processes00 Ratings8.4111 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
FreshBooks
9.4
49 Ratings
21% above category average
QuickBooks Desktop Enterprise
8.1
147 Ratings
6% above category average
Pricing8.839 Ratings8.3109 Ratings
Order entry9.337 Ratings8.4114 Ratings
Credit card processing9.641 Ratings7.7103 Ratings
Cost of goods sold10.01 Ratings8.7131 Ratings
Order Orchestration00 Ratings7.864 Ratings
End-to-end order visibility00 Ratings8.163 Ratings
Order exception Resolution00 Ratings8.149 Ratings
Payroll Management
Comparison of Payroll Management features of Product A and Product B
FreshBooks
-
Ratings
QuickBooks Desktop Enterprise
8.5
125 Ratings
12% above category average
Pay calculation00 Ratings9.2118 Ratings
Benefit plan administration00 Ratings7.971 Ratings
Direct deposit files00 Ratings8.9102 Ratings
Salary revision and increment management00 Ratings8.193 Ratings
Reimbursement management00 Ratings8.294 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
FreshBooks
-
Ratings
QuickBooks Desktop Enterprise
7.6
118 Ratings
1% above category average
Inventory tracking00 Ratings8.1114 Ratings
Automatic reordering00 Ratings7.760 Ratings
Location management00 Ratings7.675 Ratings
Manufacturing module00 Ratings7.259 Ratings
Best Alternatives
FreshBooksQuickBooks Desktop Enterprise
Small Businesses
QuickBooks Self-Employed (discontinued)
QuickBooks Self-Employed (discontinued)
Score 7.2 out of 10
QuickBooks Self-Employed (discontinued)
QuickBooks Self-Employed (discontinued)
Score 7.2 out of 10
Medium-sized Companies
Zoho Books
Zoho Books
Score 9.1 out of 10
Zoho Books
Zoho Books
Score 9.1 out of 10
Enterprises
SAP S/4HANA Cloud
SAP S/4HANA Cloud
Score 8.5 out of 10
SAP S/4HANA Cloud
SAP S/4HANA Cloud
Score 8.5 out of 10
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User Ratings
FreshBooksQuickBooks Desktop Enterprise
Likelihood to Recommend
8.4
(75 ratings)
8.4
(208 ratings)
Likelihood to Renew
7.6
(18 ratings)
8.5
(26 ratings)
Usability
9.5
(20 ratings)
9.9
(13 ratings)
Availability
10.0
(2 ratings)
10.0
(4 ratings)
Performance
8.0
(1 ratings)
10.0
(3 ratings)
Support Rating
6.0
(11 ratings)
6.0
(5 ratings)
In-Person Training
-
(0 ratings)
7.0
(1 ratings)
Online Training
-
(0 ratings)
9.1
(3 ratings)
Implementation Rating
10.0
(1 ratings)
9.5
(10 ratings)
Configurability
-
(0 ratings)
5.2
(4 ratings)
Ease of integration
-
(0 ratings)
9.1
(2 ratings)
Product Scalability
-
(0 ratings)
10.0
(3 ratings)
Vendor post-sale
-
(0 ratings)
1.3
(4 ratings)
Vendor pre-sale
-
(0 ratings)
10.0
(3 ratings)
User Testimonials
FreshBooksQuickBooks Desktop Enterprise
Likelihood to Recommend
FreshBooks
I recommend FreshBooks to anyone running a service-based business that needs invoicing, time reporting, and accounting tools. FB is adept in all three of these scenarios and isn't overly complicated like similar accounting packages I have used. I love how I can write estimates and proposals, manage the business development process from the software, and quickly convert prospects to invoiced clients.
Read full review
Intuit
QuickBooks Enterprise is great for managing our inventory, purchases and income as we receive it. We use it to help budget and plan our monthly purchases, as well as keep each location on track when it comes to their expenses. It's also used for payroll and timekeeping at each store.
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Pros
FreshBooks
  • Invoicing - FreshBooks basically ensures our accountants spend less time on invoices via its automated invoicing system, which sends invoices to our customers and clients alike and also send them regular reminders for them to pay up their bills.
  • Collecting business insights - FreshBooks enable our company analysts measure our business performances via data reports provided by FreshBooks' intuitive dashboard. Allowing us do a comparative analysis of key business metrics of a current month against past months and determine if the business is growing.
  • Expense tracker - We have recently embraced FreshBooks as an expense tracker for teams at our company branch. Thusfar, FreshBooks has performed very well, making our expense management a perfect operation; ensuring teams do not exceed their planned budget and also eliminating the need for tracking expenses on excel spreadsheets.
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Intuit
  • Generally, a mouse is not needed!
  • Updating as each transaction is posted means, in the event of a crash, power failure, whatever; all the posted transactions are securely in the data file and can be pulled up on another computer, if the computer being used crashes.
  • Reporting is generally user friendly, in that one can see the desired results by setting a few parameters for the report.
Read full review
Cons
FreshBooks
  • I can brand invoices with my business logo, but I might like to change colours of the invoices themselves to match the rest of my business documents. That isn't a major point at all, but it's something that I'd like to see.
  • Freshbooks doesn't remember the categories that similar expenses were previously assigned to. It would be nice if Freshbooks would suggest a category for an already saved vendor, to ensure the consistency of expense reporting.
  • The home page of a Freshbooks account has a great graph display of expenses and income, but it only shows the last 6 months. This is still very useful, but I'd like to be able to see this kind of graph for different periods of time.
Read full review
Intuit
  • Wish we had the ability to track gallons. We are a truck stop and need to know how many gallons we buy and sell.
  • Matching up credits in Pay Bills can be challenging, especially if you make a mistake.
  • Wish in some of the reporting that it would automatically total some columns.
  • Downloading from the bank wish it would tell you the last time you downloaded and the dates you put in so you don't download the same information twice.
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Likelihood to Renew
FreshBooks
At the current needs of our business, FreshBooks suits us perfectly - it allows online access by our accountant to the system for GST purposes, easy input of expenses and tracking of Profit and Loss statements. FreshBooks customer service is great as well - very understanding and accommodating.
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Intuit
While QuickBooks Desktop Enterprise has been an amazing tool for many years, it seems it is getting phased out for QuickBooks Online. Intuit is decreasing the level of support it offers for QuickBooks Desktop in lieu of stronger support for QuickBooks Online. Although the desktop version is robust and helpful, it seems QBO is the way of the future for bookkeeping with QuickBooks.
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Usability
FreshBooks
FreshBooks is very easy to use even for novices. If you're looking for an online accounting software that is full of features, has great aesthetics and is user-friendly, then this is definitely the software for you. I've been using it for several years now and despite being tempted to switch by other vendors, I like the feel of FreshBooks and it's mobile features.
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Intuit
QuickBooks provides all staff immediate access to the data in whatever form each person wants it. The balancing on entries prevents incorrect data entry on payables/receivables. Reports are easy to customize and save for future use. The records are easy to audit.
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Reliability and Availability
FreshBooks
FreshBooks is easy to use and always works!
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Intuit
Rating: 7 out of 10
We rate QuickBooks Desktop Enterprise's availability a 7 out of 10. For the most part, the software is dependable and available when we need it. When hosted on a properly managed local server or through a reputable third-party cloud provider, uptime is generally consistent, and routine day-to-day operations run smoothly.
However, availability challenges do arise, particularly when accessing QuickBooks remotely or during periods of high system demand. Because it's a desktop-based solution, availability is highly dependent on our internal IT infrastructure. If our network goes down, a server needs maintenance, or if there’s an issue with a remote desktop connection, access to QuickBooks can be temporarily disrupted. These outages aren’t necessarily caused by QuickBooks itself, but they do impact our experience with availability.
Additionally, we’ve occasionally experienced application errors, especially after updates or when working with large company files. While Intuit support is usually helpful in resolving these issues, they can still lead to frustrating delays—especially during critical periods like month-end closing or grant reporting deadlines.
Planned maintenance, while infrequent, also affects availability, especially when using a hosted environment. Coordination with IT or hosting providers is sometimes needed to minimize downtime.
Overall, QuickBooks Desktop Enterprise is a reliable tool, but its dependence on local infrastructure introduces more potential points of failure compared to cloud-native solutions. Enhancements in cloud-based access or hybrid models could significantly improve both accessibility and uptime. That said, with strong internal IT support or a reliable cloud hosting provider, the availability can easily rise to an 8 or 9.
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Performance
FreshBooks
No answers on this topic
Intuit
I rate QuickBooks Desktop Enterprise's performance a 5 out of 10, mainly because while it’s functional for most routine tasks, it can lag significantly when handling complex operations, large data files, or during multi-user sessions. As our organization has grown, we’ve noticed that report generation—especially for customized or multi-dimensional reports—can be slow, sometimes taking several minutes to load or refresh. This impacts productivity, particularly during key financial cycles like audits, monthly closings, or grant reporting.
Performance degradation is especially noticeable when multiple users are active in the system at the same time. Even with a solid server setup, there’s often a drop in responsiveness when more than a handful of users are generating reports or entering transactions concurrently.
We’ve also experienced some slowdowns in third-party integrations, particularly when syncing with Vena Solutions or exporting data for use in external tools. While the integrations are valuable, they occasionally stall or require workarounds, adding friction to our workflows.
In short, QuickBooks Desktop Enterprise delivers the basics well, but its performance limitations become more apparent in high-volume or complex use cases. It would benefit from better optimization for large datasets and faster processing for advanced reporting. Upgrades in system architecture—such as deeper support for cloud hosting or more efficient data handling—could significantly improve the user experience and move this rating closer to an 8.
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Support Rating
FreshBooks
I think the support level for FreshBooks is on par with a 6 because the folks behind this application do a fairly good job at providing support for their customer base. I still don't think they are at an elite level when it comes to supporting but are getting there although too slow in my opinion.
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Intuit
It takes a long time to get through to customer support. And sometimes you have to explain the situation multiple times before the rep actually understands the issue, but that's usually because the issue is complex and out of the ordinary. However, the rep is always patient, and will take as much time and effort as necessary to resolve whatever issue you're having. It's nice that they can "take over" your computer rather than having to talk you through the solution over the phone.
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In-Person Training
FreshBooks
No answers on this topic
Intuit
It is a very easy system to learn, so with the help it was even easier. QB is a good solid system, but it lacks some of the complexity other systems have. with QB you need to get additional modules to get the same functionality that other systems offer standard
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Online Training
FreshBooks
No answers on this topic
Intuit
easy to learn system, specially with some kind of support. Just like with any other system, things get lot easier if you have guidance to lead you in your search for answers. having said that, QB is very easy to use and very easy to teach. you wont spend much time memorizing where to click.
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Implementation Rating
FreshBooks
I haven't changed my mind since my first evaluation. Freshbooks is still meeting my needs, easy to use, etc.
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Intuit
If you're loading QuickBooks Enterprise Solutions onto a computer that you're going to directly log into, you should be able to do it yourself. If you are going to connect to a server through a network or remote connection, you should probably have a professional IT person set it up for you.
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Alternatives Considered
FreshBooks
FreshBooks does very well in comparison, especially since it is free software for Barclays bank users. Sage software is much worse than FreshBooks. However, Xero and QuickBooks, the market leaders, are still ahead with usability, additional features, reporting, and connection with third-party software providers. We chose FreshBooks as it does everything we require from this type of software.
Read full review
Intuit
We have selected this product as it is affordoable in terms of pricing and features too. Our clients is geeting lots of benefits by using this product. By using QuickBooks desktop client also manage the information realted to financials and also get the clear picture for the future by using the accounting information from this product.
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Scalability
FreshBooks
No answers on this topic
Intuit
I would rate QuickBooks Desktop Enterprise a 7 out of 10 for overall scalability. The product offers solid scalability features, particularly for small to mid-sized organizations like ours that are growing and need reliable multi-user access, enhanced data capacity, and cross-departmental functionality. It handles increasing transaction volumes and user growth quite well, especially with its support for up to 40 users and the ability to manage large lists (customers, vendors, accounts, etc.)—a significant improvement over QuickBooks Pro or Premier.
Its role-based permissions system also allows us to assign tailored access by department or user level, which is essential for maintaining control and security across teams like finance, HR, and program management. Additionally, features like advanced reporting, inventory management, and class tracking have helped us better manage multiple programs or sites within one system.
That said, the scalability still has some limits. For example, deploying the software across multiple physical locations or for remote teams requires additional IT infrastructure—such as hosting it on a third-party cloud server or setting up a VPN—which introduces cost and complexity. Also, while QuickBooks Desktop Enterprise can technically handle a high volume of data, performance can decline as the file size grows over time unless regular maintenance and optimization are done.
In summary, QuickBooks Desktop Enterprise scales well within its designed range, particularly for growing nonprofits and NGOs. However, organizations with distributed teams or very large, complex operations may eventually find the system’s desktop-based architecture less agile compared to cloud-native ERP platforms. With enhancements to cloud integration and remote accessibility, this rating could easily increase.
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Return on Investment
FreshBooks
  • In reality, we do not implement all of its use at the moment in order to determine an adequate ROI.
  • In our approach to the use of the system, it seems to us a considerable time saving by achieving the integration of the Mexican subsidiary with its parent located in the US.
  • Financial reports meet the necessary USGAAP requirements.
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Intuit
  • Good value for the price. The initial setup was quick and easy.
  • When properly set up and processes are followed it's decent at managing inventory which is something we had problems with. Have to have a dedicated employee to builds.
  • Rolling up costs in multi-level BOM's is a project each time we have to review costs, it's very time consuming to manually update all assemblies.
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ScreenShots

FreshBooks Screenshots

Screenshot of the dashboardScreenshot of an invoice overviewScreenshot of an example of a customizable invoiceScreenshot of an invoice appearing across devicesScreenshot of expensesScreenshot of time tracking