Paychex Flex vs. QuickBooks Desktop Enterprise

Overview
ProductRatingMost Used ByProduct SummaryStarting Price
Paychex Flex
Score 6.6 out of 10
N/A
Paychex Flex, of Paychex' Online Payroll Services, is a cloud-based human resource management and payroll platform. Paychex offers core and specialized services, and scales to meet the needs of small businesses, SMBs, and large enterprises.
$59
per month/+$4 per employee
QuickBooks Desktop Enterprise
Score 8.2 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.
$1,261
per year
Pricing
Paychex FlexQuickBooks Desktop Enterprise
Editions & Modules
Paychex Go
$59
per month/+$4 per employee
Paychex Flex Service
Contact sales team
Paychex Flex Enterprise
Contact sales team
Gold
1,261
per year
Platinum
1,522
per year
Gold with Remote Access
1,785.60
per year
Platinum with Remote Access
2,083.20
per year
Diamond
3,060.34
per year
Diamond with Remote Access
3,600.36
per year
Offerings
Pricing Offerings
Paychex FlexQuickBooks Desktop Enterprise
Free Trial
NoNo
Free/Freemium Version
NoNo
Premium Consulting/Integration Services
NoNo
Entry-level Setup FeeRequiredOptional
Additional Details
More Pricing Information
Community Pulse
Paychex FlexQuickBooks Desktop Enterprise
Considered Both Products
Paychex Flex
Chose Paychex Flex
Their prices are way better, but Paychex has actual, responsive customer support. If Square could match your support, I'd consider making the switch.
Chose Paychex Flex
Paychex is much more user friendly than many of the other payroll services that I have used.
Chose Paychex Flex
I have used Paychex Flex for seven years, the company has used it for over 40 years. I do not see us changing.
Chose Paychex Flex
I think Paychex Flex is slightly better than ADP. Paychex Flex and ADP create the same needed reports and have a lot of the same functions; however, Paychex Flex is more visually pleasing. Paychex Flex uses a tile format and is easy to get into different categories such as …
Chose Paychex Flex
Paychex flex blows this away. Lanky and confusing to use and the customer service is lacking and confusing. Multiple trouble with payments on taxes. We only used it for a short while after ADP before going to Flex. Would not consider doing in a house with all the new complex …
Chose Paychex Flex
I used ADP when I owned a much larger business with 15+ employees and weekly payroll.
The customer service was not comparable to the friendly, knowledgeable advisors that are handling my account. I feel awkward sometimes having to contacting them for simple questions considering …
Chose Paychex Flex
Most offer the same things, some offer a little less with less cost.
QuickBooks Desktop Enterprise

No answer on this topic

Top Pros
Top Cons
Features
Paychex FlexQuickBooks Desktop Enterprise
Human Resource Management
Comparison of Human Resource Management features of Product A and Product B
Paychex Flex
6.7
247 Ratings
16% below category average
QuickBooks Desktop Enterprise
-
Ratings
Employee demographic data8.0197 Ratings00 Ratings
Employment history8.1220 Ratings00 Ratings
Job profiles and administration6.8155 Ratings00 Ratings
Workflow for transfers, promotions, pay raises, etc.7.3154 Ratings00 Ratings
Organizational charting1.01 Ratings00 Ratings
Organization and location management7.9138 Ratings00 Ratings
Compliance data (COBRA, OSHA, etc.)7.5132 Ratings00 Ratings
Payroll Management
Comparison of Payroll Management features of Product A and Product B
Paychex Flex
8.5
288 Ratings
6% above category average
QuickBooks Desktop Enterprise
7.9
108 Ratings
6% above category average
Pay calculation9.0271 Ratings8.7104 Ratings
Off-cycle/On-Demand payment9.1136 Ratings00 Ratings
Benefit plan administration7.2156 Ratings7.861 Ratings
Direct deposit files9.2270 Ratings8.090 Ratings
Salary revision and increment management8.5193 Ratings7.782 Ratings
Reimbursement management7.9105 Ratings7.583 Ratings
Leave and Attendance Management
Comparison of Leave and Attendance Management features of Product A and Product B
Paychex Flex
7.0
144 Ratings
14% below category average
QuickBooks Desktop Enterprise
-
Ratings
Approval workflow6.3102 Ratings00 Ratings
Balance details7.5136 Ratings00 Ratings
Annual carry-forward and encashment7.3110 Ratings00 Ratings
Employee Self Service
Comparison of Employee Self Service features of Product A and Product B
Paychex Flex
8.5
249 Ratings
5% above category average
QuickBooks Desktop Enterprise
-
Ratings
View and generate pay and benefit information8.6228 Ratings00 Ratings
Update personal information9.0239 Ratings00 Ratings
View company policy documentation7.7111 Ratings00 Ratings
View job history8.7168 Ratings00 Ratings
Asset Management
Comparison of Asset Management features of Product A and Product B
Paychex Flex
7.8
40 Ratings
1% above category average
QuickBooks Desktop Enterprise
-
Ratings
Tracking of all physical assets7.840 Ratings00 Ratings
HR Reporting
Comparison of HR Reporting features of Product A and Product B
Paychex Flex
6.1
164 Ratings
22% below category average
QuickBooks Desktop Enterprise
-
Ratings
Report builder5.8134 Ratings00 Ratings
Pre-built reports6.8154 Ratings00 Ratings
Ability to combine HR data with external data5.683 Ratings00 Ratings
Onboarding
Comparison of Onboarding features of Product A and Product B
Paychex Flex
8.0
158 Ratings
0% below category average
QuickBooks Desktop Enterprise
-
Ratings
New hire portal8.0151 Ratings00 Ratings
Manager tracking tools7.9100 Ratings00 Ratings
Recruiting / ATS
Comparison of Recruiting / ATS features of Product A and Product B
Paychex Flex
8.5
59 Ratings
9% above category average
QuickBooks Desktop Enterprise
-
Ratings
Job Requisition Management9.732 Ratings00 Ratings
Company Website Posting9.730 Ratings00 Ratings
Publish to Social Media6.823 Ratings00 Ratings
Job Search Site Posting6.730 Ratings00 Ratings
Duplicate Candidate Prevention6.828 Ratings00 Ratings
Applicant Tracking9.633 Ratings00 Ratings
Notifications and Alerts9.853 Ratings00 Ratings
Customization
Comparison of Customization features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Desktop Enterprise
7.5
74 Ratings
6% above category average
API for custom integration00 Ratings7.857 Ratings
Plug-ins00 Ratings7.168 Ratings
Security
Comparison of Security features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Desktop Enterprise
8.3
156 Ratings
4% above category average
Single sign-on capability00 Ratings8.3118 Ratings
Role-based user permissions00 Ratings8.2154 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Desktop Enterprise
8.3
173 Ratings
9% above category average
Dashboards00 Ratings8.4148 Ratings
Standard reports00 Ratings8.6171 Ratings
Custom reports00 Ratings8.1166 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Desktop Enterprise
8.1
177 Ratings
9% above category average
Accounts payable00 Ratings8.8170 Ratings
Accounts receivable00 Ratings8.9169 Ratings
Cash management00 Ratings8.4155 Ratings
Bank reconciliation00 Ratings9.0168 Ratings
Expense management00 Ratings8.3155 Ratings
Time tracking00 Ratings6.577 Ratings
Fixed asset management00 Ratings8.1115 Ratings
Multi-currency support00 Ratings7.757 Ratings
Multi-division support00 Ratings8.093 Ratings
Regulations compliance00 Ratings8.265 Ratings
Electronic tax filing00 Ratings8.187 Ratings
Self-service portal00 Ratings6.667 Ratings
Global Financial Support00 Ratings6.432 Ratings
Primary and Secondary Ledgers00 Ratings8.161 Ratings
Intercompany Accounting00 Ratings8.175 Ratings
Localizations00 Ratings8.145 Ratings
Journals and Reconciliations00 Ratings8.9126 Ratings
Enterprise Accounting00 Ratings8.586 Ratings
Configurable Accounting00 Ratings8.383 Ratings
Centralized Rules Framework00 Ratings8.150 Ratings
Standardized Processes00 Ratings8.794 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Desktop Enterprise
7.6
104 Ratings
8% above category average
Inventory tracking00 Ratings8.1100 Ratings
Automatic reordering00 Ratings7.353 Ratings
Location management00 Ratings8.366 Ratings
Manufacturing module00 Ratings6.850 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Desktop Enterprise
8.3
129 Ratings
12% above category average
Pricing00 Ratings8.695 Ratings
Order entry00 Ratings8.6101 Ratings
Credit card processing00 Ratings7.790 Ratings
Cost of goods sold00 Ratings8.3114 Ratings
Order Orchestration00 Ratings8.255 Ratings
End-to-end order visibility00 Ratings8.352 Ratings
Order exception Resolution00 Ratings8.739 Ratings
Best Alternatives
Paychex FlexQuickBooks Desktop Enterprise
Small Businesses
Patriot Software
Patriot Software
Score 9.0 out of 10
Dext Prepare (with Receipt Bank)
Dext Prepare (with Receipt Bank)
Score 9.1 out of 10
Medium-sized Companies
Paypro Workforce Management
Paypro Workforce Management
Score 9.5 out of 10
Accounting Seed
Accounting Seed
Score 8.3 out of 10
Enterprises
Infor Human Resources
Infor Human Resources
Score 7.3 out of 10
Oracle Fusion Cloud ERP
Oracle Fusion Cloud ERP
Score 8.1 out of 10
All AlternativesView all alternativesView all alternatives
User Ratings
Paychex FlexQuickBooks Desktop Enterprise
Likelihood to Recommend
7.7
(298 ratings)
8.5
(188 ratings)
Likelihood to Renew
8.9
(42 ratings)
9.8
(17 ratings)
Usability
8.0
(240 ratings)
9.1
(11 ratings)
Availability
9.3
(10 ratings)
10.0
(4 ratings)
Performance
9.1
(10 ratings)
10.0
(3 ratings)
Support Rating
7.7
(245 ratings)
6.0
(5 ratings)
In-Person Training
4.5
(1 ratings)
7.0
(1 ratings)
Online Training
7.0
(4 ratings)
9.1
(3 ratings)
Implementation Rating
9.4
(11 ratings)
9.0
(8 ratings)
Configurability
7.6
(8 ratings)
10.0
(3 ratings)
Ease of integration
9.1
(3 ratings)
9.1
(2 ratings)
Product Scalability
9.3
(10 ratings)
10.0
(3 ratings)
Vendor post-sale
8.9
(31 ratings)
9.0
(3 ratings)
Vendor pre-sale
9.2
(32 ratings)
10.0
(3 ratings)
User Testimonials
Paychex FlexQuickBooks Desktop Enterprise
Likelihood to Recommend
Paychex, Inc.
In my experience, Paychex Flex is well suited for small to medium sized businesses. It has been helpful in streamlining the onboarding process and it is easy to update and maintain employee profiles and records. It has worked will in a non-profit environment where there is clergy pay and housing, which can get quite complicated. I cannot think of a scenario where it would be less appropriate.
Read full review
Intuit
QuickBooks Desktop Enterprise is very flexible. When you have made a mistake, most mistakes are fixed easily. This is wonderful if you know what you are doing. If you don't know what you are doing QuickBooks Desktop Enterprise gives the user, the ability to do many things incorrectly. If you are not an accountant, you don't know you are doing it incorrectly. That can be a problem.
Read full review
Pros
Paychex, Inc.
  • I like I can enter payroll and if I need to leave the program, I can resume at a later time and my information is saved.
  • I like the analytics & reports features.
  • I like how all my employees have easy access to their portal.
Read full review
Intuit
  • Detailed organization of financial information
  • Several security measures and double check systems to ensure incorrect entries aren't made. This prevents accidental errors and protects the company from fraud.
  • Ease of overall use
  • Reporting can be as detailed or as general as you prefer. Each report allows you to look at the overall picture or access specific details of each aspect of the company financials.
Read full review
Cons
Paychex, Inc.
  • Reporting writing is difficult to figure out
  • Employee turnover inside Paychex was a problem, until we were assigned to Neil Williams - since that time it has settled down
  • Pressure to convert personal connection with payroll advisor to using automated service
Read full review
Intuit
  • I would like to see more ways to customize reports and have that process be more user friendly.
  • I would like to see the process of creating year end giving statements be made more user friendly. Since I only do it once a year, I have to figure the process out every year.
Read full review
Likelihood to Renew
Paychex, Inc.
Overall I like the features that Paychex Flex offers. I am sure that there are other features that I am unaware of, so I am excited to see if there is more that Flex is capable of to make my job easier. The basic features are really user friendly and easy to access. If there ever is an issue customer service is great
Read full review
Intuit
We've been using QuickBooks Enterprise Solutions from when the business started, 11 years ago. I don't see us changing programs any time soon as it is working pretty well for us now. It would be extremely time consuming to start from scratch with a new accounting or inventory management program.
Read full review
Usability
Paychex, Inc.
Some things could be streamlined. For example, we could do custom options for the "add items" tab which has so many options that we never use. "Medical Pay" could be something that the system remembers for the applicable employees. Salaried employees' salaries should definitely be auto-filled. Overall the system works well but I think it could be improved to be easier to use and read.
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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
Paychex, Inc.
We have not experienced any difficulties with unplanned outages. Notifications are always made for outages, and they do not effect normal business operations.
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Intuit
They have always been available to meet our needs when we need it. We have had zero complaints with getting the assistance we need.
Read full review
Performance
Paychex, Inc.
Unless there is lag time within the internet, the Paychex Flex website loads exceptional fast, pages load quickly and reports that I need to print or download load quickly. If I need to create a specialized report, once I complete it I receive an e-mail telling me my report is ready to be downloaded. Changing between web pages is fast as well.
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Intuit
QB is a good and reliable system. We probably should have explore the other modules rather that jump in to the conclusion that we needed a new ERP.
Read full review
Support Rating
Paychex, Inc.
Our dedicated representative is one of the main reasons we are sticking with Paychex Flex. If it were not for this person, other platforms could provide the same/similar functionality. It is the ability to speak with someone that understands our business and is willing to get questions answered in a timely fashion that keeps us with Paychex Flex.
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Intuit
Very rare do I call the Quickbooks Enterprise Solutions support staff and I get a customer service associate quickly. On average, my wait time is near an hour, and at times even longer. After spending the first three minutes discussing my problem, they then begin to poke and prod around, sometimes the questions continue. But 80% of the time, the problem is over their head and they have to escalate the issue. The only problem is this escalation arrives usually after spending forty-five minutes poking and proding around but learning nothing. In short, my experience is rarely all that well, let alone great
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In-Person Training
Paychex, Inc.
We did online training only
Read full review
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
Paychex, Inc.
It was easy to understand and follow along. I do like the informational videos that we can utilize before we opt to call in for customer service support. It has made a difference since sometimes that resolves the issue I may have had and saved myself a phone call to Paychex support.
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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
Paychex, Inc.
Implementation was very smooth. The most cumbersome task was entering the current employees into the system during initial set up, but Paychex staff handled most of that and verified against prior system reports as well as internal reports provided to ensure 100% accuracy.
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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
Paychex, Inc.
We still use QB Desktop Pro to maintain a Check Register / Overall Balance for the company, but once having tried QB Payroll Online for about 3 months prior to finding Paychex Flex I can tell you that there's just no comparison. QB online is VERY EXPENSIVE and not so user-friendly. I hated every minute of those 6 payrolls we ran through QB online.
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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
Paychex, Inc.
Employees can log in at home and get up to date information on their FSA balance and any medical bill reimbursements they may have uploaded. At renewal time they have the ability to make changes to their FSA or for new employees star the enrollment.
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Intuit
It has worked for our small company in every way. We have very little issues with the software and when we have had problems, Intuit has stepped up and resolved in promptly.
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Return on Investment
Paychex, Inc.
  • I do not believe we have saved anything additionally. The time we've had to spend to get things to hopefully work is sad. This is the reason we've had to turn off all extra "products" of Paychex Flex. Time and Attendance is horrible. Benefits management is horrible. The user experience is horrible.
  • One thing I do not understand is why are updates for states, cities, counties, school districts, etc. not automatically updated? Should we not get a big red flag if we have an employee living/working, being paid in CA, but they aren't set up for CA sick time? If it is required to be on the paycheck stub to show the balance of the sick time, why would we not be notified that we are out of compliance?
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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

Paychex Flex Screenshots

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