Paychex vs. QuickBooks Desktop Premier

Overview
ProductRatingMost Used ByProduct SummaryStarting Price
Paychex
Score 6.8 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.N/A
QuickBooks Desktop Premier
Score 8.0 out of 10
N/A
QuickBooks Desktop Premier is an installed version of QuickBooks for general business, contractors, manufacturing and warehouse accounting, as well as nonprofits, professional services, and retail.N/A
Pricing
PaychexQuickBooks Desktop Premier
Editions & Modules
Paychex Flex Pro
Custom Pricing
per month/+$4 per employee
HR Pro
Custom Pricing
HR PEO
Custom Pricing
Paychex Flex Select
Custom Pricing
Paychex Flex Enterprise
Custom Pricing
No answers on this topic
Offerings
Pricing Offerings
PaychexQuickBooks Desktop Premier
Free Trial
NoNo
Free/Freemium Version
NoNo
Premium Consulting/Integration Services
NoNo
Entry-level Setup FeeRequiredNo setup fee
Additional Details
More Pricing Information
Community Pulse
PaychexQuickBooks Desktop Premier
Considered Both Products
Paychex
Chose Paychex
They used ADP before I started, but the previous office manager did tell me that Paychex was more streamlined, more user friendly, and she loved the features that Paychex had to offer over ADP. I will say in my experience, that customer service is a lot quicker with Paychex.
Chose Paychex
I changed from Paychex Preview to Paychex Flex and have not evaluated other products.
Chose Paychex
Most of the reporting is a little easier to find and create in Paychex Flex. Most of the web interfaces for submitting payroll are fairly easy just like Paychex Flex.
Chose Paychex
I do not recall the names of the software systems but they didn't compare in ease of use or functionality.
Chose Paychex
Paychex Flex is geared towards a larger and more sophisticated organization than Xero. Xero is really only the better solution to an organization that was previously keeping its books in Excel. Paychex Flex helps companies program future payroll decisions and inputs ahead of …
Chose Paychex
I was not here when the decision was made to move to the Paychex Flex system. I had used Paychex as a payroll processing company at a previous job, so it has been interesting and beneficial to see the other things they can offer. It is also a much better team behind it than …
QuickBooks Desktop Premier

No answer on this topic

Features
PaychexQuickBooks Desktop Premier
Human Resource Management
Comparison of Human Resource Management features of Product A and Product B
Paychex
6.7
272 Ratings
19% below category average
QuickBooks Desktop Premier
-
Ratings
Employee demographic data7.8219 Ratings00 Ratings
Employment history8.1242 Ratings00 Ratings
Job profiles and administration7.8177 Ratings00 Ratings
Workflow for transfers, promotions, pay raises, etc.7.8172 Ratings00 Ratings
Organizational charting1.01 Ratings00 Ratings
Organization and location management7.5158 Ratings00 Ratings
Compliance data (COBRA, OSHA, etc.)6.7146 Ratings00 Ratings
Payroll Management
Comparison of Payroll Management features of Product A and Product B
Paychex
7.7
313 Ratings
5% below category average
QuickBooks Desktop Premier
8.5
54 Ratings
12% above category average
Pay calculation8.0295 Ratings9.252 Ratings
Off-cycle/On-Demand payment7.1153 Ratings00 Ratings
Benefit plan administration6.9174 Ratings8.425 Ratings
Direct deposit files8.3294 Ratings8.242 Ratings
Salary revision and increment management8.0209 Ratings8.433 Ratings
Reimbursement management7.7118 Ratings8.436 Ratings
Leave and Attendance Management
Comparison of Leave and Attendance Management features of Product A and Product B
Paychex
7.3
159 Ratings
11% below category average
QuickBooks Desktop Premier
-
Ratings
Approval workflow7.3113 Ratings00 Ratings
Balance details7.5151 Ratings00 Ratings
Annual carry-forward and encashment7.0119 Ratings00 Ratings
Employee Self Service
Comparison of Employee Self Service features of Product A and Product B
Paychex
7.8
270 Ratings
5% below category average
QuickBooks Desktop Premier
-
Ratings
View and generate pay and benefit information7.7248 Ratings00 Ratings
Update personal information7.9260 Ratings00 Ratings
View company policy documentation7.7121 Ratings00 Ratings
View job history7.9184 Ratings00 Ratings
Asset Management
Comparison of Asset Management features of Product A and Product B
Paychex
4.9
43 Ratings
49% below category average
QuickBooks Desktop Premier
-
Ratings
Tracking of all physical assets4.943 Ratings00 Ratings
HR Reporting
Comparison of HR Reporting features of Product A and Product B
Paychex
5.9
177 Ratings
24% below category average
QuickBooks Desktop Premier
-
Ratings
Report builder6.3147 Ratings00 Ratings
Pre-built reports6.3165 Ratings00 Ratings
Ability to combine HR data with external data5.191 Ratings00 Ratings
Onboarding
Comparison of Onboarding features of Product A and Product B
Paychex
6.4
173 Ratings
22% below category average
QuickBooks Desktop Premier
-
Ratings
New hire portal6.7165 Ratings00 Ratings
Manager tracking tools6.1109 Ratings00 Ratings
Recruiting / ATS
Comparison of Recruiting / ATS features of Product A and Product B
Paychex
5.1
70 Ratings
42% below category average
QuickBooks Desktop Premier
-
Ratings
Job Requisition Management5.536 Ratings00 Ratings
Company Website Posting5.234 Ratings00 Ratings
Publish to Social Media4.728 Ratings00 Ratings
Job Search Site Posting5.235 Ratings00 Ratings
Duplicate Candidate Prevention4.734 Ratings00 Ratings
Applicant Tracking4.839 Ratings00 Ratings
Notifications and Alerts5.964 Ratings00 Ratings
Customization
Comparison of Customization features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Premier
7.5
24 Ratings
1% below category average
API for custom integration00 Ratings8.017 Ratings
Plug-ins00 Ratings7.024 Ratings
Security
Comparison of Security features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Premier
8.4
58 Ratings
2% above category average
Single sign-on capability00 Ratings8.550 Ratings
Role-based user permissions00 Ratings8.349 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Premier
8.3
69 Ratings
6% above category average
Dashboards00 Ratings8.858 Ratings
Standard reports00 Ratings8.468 Ratings
Custom reports00 Ratings7.766 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Premier
7.8
72 Ratings
2% above category average
Accounts payable00 Ratings8.470 Ratings
Accounts receivable00 Ratings8.671 Ratings
Cash management00 Ratings8.765 Ratings
Bank reconciliation00 Ratings8.869 Ratings
Expense management00 Ratings8.868 Ratings
Time tracking00 Ratings7.535 Ratings
Fixed asset management00 Ratings6.249 Ratings
Multi-currency support00 Ratings7.623 Ratings
Multi-division support00 Ratings8.239 Ratings
Regulations compliance00 Ratings8.224 Ratings
Electronic tax filing00 Ratings7.936 Ratings
Self-service portal00 Ratings5.923 Ratings
Global Financial Support00 Ratings6.09 Ratings
Primary and Secondary Ledgers00 Ratings7.014 Ratings
Intercompany Accounting00 Ratings8.017 Ratings
Localizations00 Ratings7.76 Ratings
Journals and Reconciliations00 Ratings8.825 Ratings
Enterprise Accounting00 Ratings8.413 Ratings
Configurable Accounting00 Ratings8.015 Ratings
Centralized Rules Framework00 Ratings7.410 Ratings
Standardized Processes00 Ratings8.415 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Premier
8.0
43 Ratings
9% above category average
Inventory tracking00 Ratings8.342 Ratings
Automatic reordering00 Ratings7.321 Ratings
Location management00 Ratings8.825 Ratings
Manufacturing module00 Ratings7.722 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Premier
8.2
47 Ratings
9% above category average
Pricing00 Ratings8.037 Ratings
Order entry00 Ratings7.838 Ratings
Credit card processing00 Ratings9.134 Ratings
Cost of goods sold00 Ratings8.943 Ratings
Order Orchestration00 Ratings7.58 Ratings
End-to-end order visibility00 Ratings8.59 Ratings
Order exception Resolution00 Ratings7.56 Ratings
Best Alternatives
PaychexQuickBooks Desktop Premier
Small Businesses
Dayforce Powerpay
Dayforce Powerpay
Score 9.3 out of 10
QuickBooks Self-Employed (discontinued)
QuickBooks Self-Employed (discontinued)
Score 6.0 out of 10
Medium-sized Companies
Paypro Workforce Management
Paypro Workforce Management
Score 9.1 out of 10
Zoho Books
Zoho Books
Score 9.1 out of 10
Enterprises
PeopleStrong
PeopleStrong
Score 10.0 out of 10
SAP Cloud ERP
SAP Cloud ERP
Score 8.6 out of 10
All AlternativesView all alternativesView all alternatives
User Ratings
PaychexQuickBooks Desktop Premier
Likelihood to Recommend
6.2
(321 ratings)
8.3
(75 ratings)
Likelihood to Renew
1.2
(44 ratings)
7.5
(14 ratings)
Usability
6.7
(264 ratings)
8.9
(26 ratings)
Availability
5.5
(12 ratings)
10.0
(6 ratings)
Performance
7.1
(12 ratings)
9.0
(5 ratings)
Support Rating
6.1
(264 ratings)
4.0
(13 ratings)
In-Person Training
4.5
(1 ratings)
-
(0 ratings)
Online Training
8.3
(4 ratings)
1.0
(1 ratings)
Implementation Rating
5.3
(13 ratings)
7.2
(7 ratings)
Configurability
5.0
(9 ratings)
9.0
(2 ratings)
Ease of integration
9.1
(3 ratings)
7.0
(1 ratings)
Product Scalability
5.9
(12 ratings)
9.0
(5 ratings)
Vendor post-sale
2.2
(33 ratings)
6.0
(1 ratings)
Vendor pre-sale
3.2
(34 ratings)
6.0
(2 ratings)
User Testimonials
PaychexQuickBooks Desktop Premier
Likelihood to Recommend
Paychex Inc.
Paychex is great option for smaller employers as the site offers perk benefits to employees at no cost to the employer. I don't see anything like this being offered at competitors such as ADP RUN/Total Source, Bamboo, Trinet, Justworks or Gusto. Also, the initial set up is relatively easy and the dedicated support for set up is great along with our regular dedicated payroll support.
Read full review
Intuit
We really think that ANY typical business would be a reasonable fit for QuickBooks Desktop Premier. While not necessary, even a comparatively unexperienced accounting person could look at the "Home" screen and follow their nose thru typical daily accounting processes without much detailed knowledge. Reporting is simple, looking up customer info and prior transactions is simple, looking up vendors and prior payments is simple... all in all, quite straightforward. I really can't think of an instance where it would be 'less appropriate'.
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Pros
Paychex Inc.
  • It provides a well account of Retirement Plan Account Information.
  • Alerts are sent to email when there is new information to access.
  • Employee access both online and thru app.
  • Paperless options.
  • Easy and quick access to paystubs and tax forms.
  • Easy employee retirement management.
Read full review
Intuit
  • Employment - it makes creating paychecks a snap and tracks taxes.
  • Invoicing - they have a straightforward approach to creating invoices and you can even email them to your customers.
  • Customers - the program makes tracking customer information and balances easy.
Read full review
Cons
Paychex Inc.
  • I understand logging you out is a security function, but I'd prefer it not to log you out so soon.
  • The training we received for the team's meeting was subpar, in my opinion. Probably better geared for people with little to no computer experience. Very slow pace; we could have easily received all of this from some tutorials in a few minutes.
Read full review
Intuit
  • Support for older versions of QuickBooks ends after three years, then users must purchase the newest version at full price. Renewals should be deeply discounted for existing users.
  • I would like to see better in-product inventory tracking, so we can choose LIFO or FIFO rather than the ambiguous "average cost" method.
  • I would like to be able to assign payroll taxes to jobs for better job costing.
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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
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Intuit
Because we have been extremely happy with the product and our organization tends to be creatures of habit. We rarely leave a product that works this well for the latest and greatest. Typically we follow the "if it's not broken, don't fix it rule". While QB does make changes we typically just roll with it. If we do find something we don't like we work through it until we fully understand its functionality.
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Usability
Paychex Inc.
Employee usability is very good and user-friendly. For the most part, the employer usability is good, but for complicated rules and policies, it requires technical assistance, which in our case, was clunky and slow in implementation. Once is place, everything works as it should
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Intuit
We switched to a more "robust" software program with the hiring of a new CFO. The migration of historical data and ancillary information has been cumbersome and riddle with errors and issues. In hindsight much of what the new software program was touted to accomplish is not come to fruition. QB Desktop Premier was sufficient for the organization needs
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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
This is very reliable software, the desktop version is fast. If there is a problem, it is most likely on your own hardware!
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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
It takes forever to load.
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Support Rating
Paychex Inc.
Chat has been helpful but the person I chat with isn't always able to help me with my questions. Phone support is ok, depending on your payroll specialist. We have a great one currently, but the few before that were never available and did not return calls.
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Intuit
This is where QuickBooks falls short. Many times my staff has had questions that have not been able to get resolved easily with a chat or call. I personally have had more general questions that have not been answered easily as well. I think QuickBooks needs to provide the resources of having readily accessible help in order to make it simpler to get solutions.
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In-Person Training
Paychex Inc.
We did online training only
Read full review
Intuit
No answers on this topic
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
No answers on this topic
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
It is important to do your research. There are tutorial videos online that could help new user of this accounting system. These tutorials are straightforward and easily understandable.
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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
QuickBooks Premier handles most of my business functions efficiently in one package. It is not my "everything." I use Replicon for time rather than QuickBooks. I don't want my WIP data interfering with my accounting. I use PaySimple for it's web interface and back office processing. I don't have security issues since I don't have any credit card data in my possession. With today's identity theft environment, I have to protect myself as much as I can. Not having credit card data in my accounting software lets me sleep much better at night. Quicken will do basic accounting but does not have all the double entry accounting systems contained in QuickBooks. QuickBooks Online does much of the basic business functions but I don't like the pricing structure. As a professional accountant, that is very important to me. Bill.com provided a good service but the ability of QuickBooks to add bills and receipts to transactions makes it redundant.
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Scalability
Paychex Inc.
I generally do payroll at the office, however I have had to go remote due to internet issues and also had to take payroll on vacation with me. Very easy to log in wherever you are and manage your TAA and payroll
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Intuit
They're getting better. Still room for improvement.
Read full review
Return on Investment
Paychex Inc.
  • With Paychex Flex we have been able to improve our compliance with required documentation for new/rehires
  • Moving everyone to direct deposit and mobile clock in/out eliminated lines at punching stations and paycheck pickup stations
  • Lost checks is a thing of the past
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Intuit
  • Most of our business clients use QuickBooks which makes it efficient for us to work on clients that use the program. We can import QuickBooks data into our software which adds efficiencies to our tax practice.
  • Having staff that are familiar with the software enables our firm to provide quality service to the clients that use QuickBooks.
  • We receive referrals from satisfied QuickBooks clients.
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ScreenShots

Paychex Screenshots

Screenshot of Paychex Payroll DashboardScreenshot of Employee Background ChecksScreenshot of Paychex HR DashboardScreenshot of Paychex Flex Perks