Paychex vs. QuickBooks Desktop Pro

Overview
ProductRatingMost Used ByProduct SummaryStarting Price
Paychex
Score 6.5 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 Pro
Score 8.3 out of 10
N/A
Quickbooks Desktop Pro is accounting software from Intuit, Inc. It includes core accounting features, plus analytics and exportable reports. It is offered in on-premise and SaaS forms.N/A
Pricing
PaychexQuickBooks Desktop Pro
Editions & Modules
Paychex Go
$59
per month/+$4 per employee
Paychex Flex Service
Contact sales team
Paychex Flex Enterprise
Contact sales team
No answers on this topic
Offerings
Pricing Offerings
PaychexQuickBooks Desktop Pro
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 Pro
Considered Both Products
Paychex
Chose Paychex
I use QuickBooks Desktop Pro and QuickBooks Online for a few of my companies, however the times I've briefly looked into them for payroll services I couldn't picture making the transition. Additionally, when issues arise with those companies, (for other things like merchant …
Chose Paychex
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 …
Chose Paychex
In our small business, Quickbooks was like a gorilla in the office. Far too complicated for simple payroll implementation and production on a bi-weekly basis. Paychex Flex is far superior and well-suited to our needs.
Chose Paychex
I previously used Quickbooks payrolls. I will never go back to that system for payroll. Paychex Flex is easier to use and more reliable.
Chose Paychex
Paychex far exceeds the QuickBook payroll system I used our first year. QuickBooks did not handle local taxes and I was responsible for filing those reports and returns.
Chose Paychex
Paychex Flex takes care of all the reporting to the various tax reporting agencies, which gives me peace of mind that everything is being taken care of. ADP also does the same thing, but Paychex Flex is a little easier to be in contact with as they are always available. …
Chose Paychex
Paychex Flex is always up to date and user friendly.
Chose Paychex
Paychecx Flex is much more Affordable and efficient. Hard to choose any other company when using Paychex is a breeze.
Chose Paychex
Paychex is just right for our sized business. We do not need expanded features, just an ability to process payroll and pay taxes. We looked at Paycor, ADP, QuickBooks, Ahola and thought Paychex was the best value for what we needed.
Chose Paychex
We used a local payroll company before Paychex. I appreciate the online aspects and the ability of employees to access their own info.
Chose Paychex
ADP is more user friendly and the customer service is better than Paychex Flex. The sales rep. marketed Paychex Flex as being just like RUN but they still need to grow by leaps and bounds to catch up to RUN's reports, interface, and customer service.
Chose Paychex
I selected Paychex because they are the company my accountant steered me to. As far as I am concerned, they are perfect for me. I have been more than satisfied with their services for many years and I expect to remain with them as long as I remain in business.
QuickBooks Desktop Pro
Chose QuickBooks Desktop Pro
QuickBooks Desktop Pro is top-notch accounting software. It allows for a good bit of customization and drilling down on the reports. I've not had to use their support as our accountant and his IT staff are certified with Intuit. A little over one year ago, I started cloud-based …
Features
PaychexQuickBooks Desktop Pro
Human Resource Management
Comparison of Human Resource Management features of Product A and Product B
Paychex
6.5
268 Ratings
22% below category average
QuickBooks Desktop Pro
-
Ratings
Employee demographic data7.7215 Ratings00 Ratings
Employment history8.1239 Ratings00 Ratings
Job profiles and administration7.5173 Ratings00 Ratings
Workflow for transfers, promotions, pay raises, etc.7.4168 Ratings00 Ratings
Organizational charting1.01 Ratings00 Ratings
Organization and location management7.4155 Ratings00 Ratings
Compliance data (COBRA, OSHA, etc.)6.6144 Ratings00 Ratings
Payroll Management
Comparison of Payroll Management features of Product A and Product B
Paychex
7.6
310 Ratings
7% below category average
QuickBooks Desktop Pro
6.9
69 Ratings
9% below category average
Pay calculation8.1292 Ratings6.664 Ratings
Off-cycle/On-Demand payment6.7150 Ratings00 Ratings
Benefit plan administration6.8171 Ratings6.638 Ratings
Direct deposit files8.3291 Ratings7.056 Ratings
Salary revision and increment management7.8207 Ratings6.652 Ratings
Reimbursement management7.6116 Ratings7.554 Ratings
Leave and Attendance Management
Comparison of Leave and Attendance Management features of Product A and Product B
Paychex
7.1
158 Ratings
14% below category average
QuickBooks Desktop Pro
-
Ratings
Approval workflow7.0112 Ratings00 Ratings
Balance details7.4150 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
7.7
267 Ratings
6% below category average
QuickBooks Desktop Pro
-
Ratings
View and generate pay and benefit information7.7245 Ratings00 Ratings
Update personal information7.9257 Ratings00 Ratings
View company policy documentation7.5119 Ratings00 Ratings
View job history7.7181 Ratings00 Ratings
Asset Management
Comparison of Asset Management features of Product A and Product B
Paychex
5.4
43 Ratings
38% below category average
QuickBooks Desktop Pro
-
Ratings
Tracking of all physical assets5.443 Ratings00 Ratings
HR Reporting
Comparison of HR Reporting features of Product A and Product B
Paychex
6.0
175 Ratings
23% below category average
QuickBooks Desktop Pro
-
Ratings
Report builder6.4145 Ratings00 Ratings
Pre-built reports6.4164 Ratings00 Ratings
Ability to combine HR data with external data5.291 Ratings00 Ratings
Onboarding
Comparison of Onboarding features of Product A and Product B
Paychex
6.2
171 Ratings
25% below category average
QuickBooks Desktop Pro
-
Ratings
New hire portal6.8164 Ratings00 Ratings
Manager tracking tools5.6106 Ratings00 Ratings
Recruiting / ATS
Comparison of Recruiting / ATS features of Product A and Product B
Paychex
5.3
68 Ratings
37% below category average
QuickBooks Desktop Pro
-
Ratings
Job Requisition Management5.736 Ratings00 Ratings
Company Website Posting5.534 Ratings00 Ratings
Publish to Social Media4.928 Ratings00 Ratings
Job Search Site Posting5.335 Ratings00 Ratings
Duplicate Candidate Prevention5.034 Ratings00 Ratings
Applicant Tracking5.139 Ratings00 Ratings
Notifications and Alerts5.362 Ratings00 Ratings
Customization
Comparison of Customization features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Pro
6.0
43 Ratings
25% below category average
API for custom integration00 Ratings6.735 Ratings
Plug-ins00 Ratings5.339 Ratings
Security
Comparison of Security features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Pro
8.3
101 Ratings
1% above category average
Single sign-on capability00 Ratings8.382 Ratings
Role-based user permissions00 Ratings8.495 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Pro
8.5
117 Ratings
8% above category average
Dashboards00 Ratings8.4100 Ratings
Standard reports00 Ratings8.9117 Ratings
Custom reports00 Ratings8.3114 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Pro
7.7
124 Ratings
1% above category average
Accounts payable00 Ratings9.2119 Ratings
Accounts receivable00 Ratings9.2121 Ratings
Cash management00 Ratings9.1107 Ratings
Bank reconciliation00 Ratings9.6119 Ratings
Expense management00 Ratings9.3108 Ratings
Time tracking00 Ratings7.551 Ratings
Fixed asset management00 Ratings6.169 Ratings
Multi-currency support00 Ratings7.431 Ratings
Multi-division support00 Ratings8.858 Ratings
Regulations compliance00 Ratings8.042 Ratings
Electronic tax filing00 Ratings8.455 Ratings
Self-service portal00 Ratings6.341 Ratings
Global Financial Support00 Ratings4.517 Ratings
Primary and Secondary Ledgers00 Ratings6.740 Ratings
Intercompany Accounting00 Ratings8.343 Ratings
Localizations00 Ratings4.519 Ratings
Journals and Reconciliations00 Ratings8.776 Ratings
Enterprise Accounting00 Ratings7.138 Ratings
Configurable Accounting00 Ratings7.647 Ratings
Centralized Rules Framework00 Ratings6.527 Ratings
Standardized Processes00 Ratings8.455 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Pro
6.1
59 Ratings
21% below category average
Inventory tracking00 Ratings6.356 Ratings
Automatic reordering00 Ratings6.335 Ratings
Location management00 Ratings6.332 Ratings
Manufacturing module00 Ratings5.518 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Desktop Pro
7.1
77 Ratings
7% below category average
Pricing00 Ratings7.755 Ratings
Order entry00 Ratings8.655 Ratings
Credit card processing00 Ratings7.651 Ratings
Cost of goods sold00 Ratings8.363 Ratings
Order Orchestration00 Ratings5.520 Ratings
End-to-end order visibility00 Ratings6.523 Ratings
Order exception Resolution00 Ratings5.518 Ratings
Best Alternatives
PaychexQuickBooks Desktop Pro
Small Businesses
Dayforce Powerpay
Dayforce Powerpay
Score 9.4 out of 10
QuickBooks Self-Employed (discontinued)
QuickBooks Self-Employed (discontinued)
Score 7.3 out of 10
Medium-sized Companies
Paypro Workforce Management
Paypro Workforce Management
Score 9.7 out of 10
Zoho Books
Zoho Books
Score 9.1 out of 10
Enterprises
PeopleStrong
PeopleStrong
Score 9.9 out of 10
SAP S/4HANA Cloud
SAP S/4HANA Cloud
Score 8.5 out of 10
All AlternativesView all alternativesView all alternatives
User Ratings
PaychexQuickBooks Desktop Pro
Likelihood to Recommend
6.7
(323 ratings)
8.5
(135 ratings)
Likelihood to Renew
1.6
(44 ratings)
8.0
(19 ratings)
Usability
7.0
(264 ratings)
9.2
(42 ratings)
Availability
6.0
(12 ratings)
8.3
(2 ratings)
Performance
7.2
(12 ratings)
-
(0 ratings)
Support Rating
6.6
(265 ratings)
1.2
(29 ratings)
In-Person Training
4.5
(1 ratings)
10.0
(1 ratings)
Online Training
8.2
(4 ratings)
-
(0 ratings)
Implementation Rating
5.7
(13 ratings)
9.0
(6 ratings)
Configurability
5.2
(9 ratings)
-
(0 ratings)
Ease of integration
9.1
(3 ratings)
-
(0 ratings)
Product Scalability
6.7
(12 ratings)
8.0
(1 ratings)
Vendor post-sale
2.8
(33 ratings)
-
(0 ratings)
Vendor pre-sale
3.8
(34 ratings)
-
(0 ratings)
User Testimonials
PaychexQuickBooks Desktop Pro
Likelihood to Recommend
Paychex Inc.
For the most part, Paychex Flex is a very good payroll system and is well suited for a small business. Most basic features are simple and user friendly. For businesses that have hourly employees, its timeclock system is a good feature. For businesses that have a large number of employees and more complicated rules and policies, it might not be as appropriate because of the difficulty to set up for these rules and policies
Read full review
Intuit
For a small business, QuickBooks Desktop Pro is great! For a larger, more complex business, another system may be more beneficial. We actually run multiple businesses on QuickBooks Desktop Pro, but all are very small. The help feature is sometimes so beneficial, and sometimes it seems like you just can't get the right answer and need to find a workaround - but this is usually for more complex issues.
Read full review
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
  • It is easy to manage and adjust inventory on hand.
  • It is easy to make reports and customize them to your needs.
  • We also use it to pay our employees directly.
  • It is easy to make year-to-year comparisons to see where we can make improvements and the current financial situation.
Read full review
Cons
Paychex Inc.
  • When it comes to audit reports, Paychex Flex could improve on helping clients locate the correct reports for audit purposes more easily
  • When a client receives a discount, it would be helpful if the discount were automatically provided each year, or if the Paychex rep proactively reached out to the client first, versus the client having to call and request that the discount continue.
  • It would be helpful if the invoice was emailed to the client versus the client logging in to access invoices.
Read full review
Intuit
  • QuickBooks Desktop Pro has been around for a few years and after an update[,] they force you to look at the changes/updates before you can use [them] after updating.
  • QuickBooks Desktop Pro does not have 2FA.
  • QuickBooks Desktop Pro should offer a way to store backups to a personal cloud without having to map a local network drive.
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
I'd love to keep using it, and do intend to - though we've not been pleased with price increases over the past several years. In fact, we used to subscribe to the payroll service, but QuickBooks priced themselves out of reach for us, so we discontinued that. Currently, pricing would be the primary reason for NOT renewing, if we didn't.
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.
Read full review
Intuit
The set up was quite easy. I took some online training causes, and figured our the rest pretty quickly. The only issue I had during the implementation process was it was very hard to change some of the GL Account name to reflect the needs of a non-profit organization, such as Net Assets. At the end I had to scratch what I did, and used the existing formats that the third-party bookkeeping firm shared. Everything else is simple and easy to manage and implement.
Read full review
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.
Read full review
Intuit
I haven't experienced a time when QuickBooks Pro was unavailable when I needed it in the entire 20 years of using the software
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.
Read full review
Intuit
No answers on this topic
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.
Read full review
Intuit
They are awful. Intuit doesn't spend real money on support. They appear to have typically said, first-level script readers who are sending messages to the senior people for anything even a little bit difficult. Many of them don't speak particularly good English. Considering that they recently doubled (or, if you are paying annually, tripled) their pricing, and touted as one of the benefits that it includes [..] support, it's a real ripoff. However, we have to use the product because it is ubiquitous. I look forward to the day a competitor comes up with something good enough, which has excellent support, that matches all the features QuickBooks Desktop Pro currently has [...] or at least gives us a way to have all the functionality we currently have without excessive sacrifice [...] so that we can switch. I was very satisfied with QuickBooks for many years. This latest [rise] in price, and their sheer gall at touting the benefit of the 100 to 200% increase as being [the] inclusion of support, is what turned me so far against them.
Read full review
In-Person Training
Paychex Inc.
We did online training only
Read full review
Intuit
Best thing I ever did was to attend a two day training seminar on QuickBooks, I learned an immense amount in a short time with hands on training by experts. I strongly recommend such training for anyone using any part of the software. It will pay for itself in the first month.
Read full review
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.
Read full review
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.
Read full review
Intuit
We implemented the software ourselves. The training we received on the software was done by taking a community course teaching us how to use QuickBooks. It allowed me to get started with some basics of how to use the program and have not needed much assistance since completing the course work.
Read full review
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.
Read full review
Intuit
We tried switching from QuickBooks Desktop Pro to QuickBooks Online, but there were a lot of issues and bugs so we ultimately decided to stay with Desktop Pro. Unfortunately, we are losing a lot of Online Banking capabilities on 5/31 as we have an older version of QB, but we plan to stick with Desktop Pro. In terms of invoicing, SaaSOptics beats QuickBooks in almost all aspects as it's all automated and takes seconds to create and send invoices. However, SaaSOptics is not really a full ERP program so it wouldn't serve us as a main bookkeeping software like QB.
Read full review
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
Read full review
Intuit
No answers on this topic
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?
Read full review
Intuit
  • Training time is low compared to other accounting packages
  • It was difficult to adapt to DCAA requirements, [which] required [the] hiring of [a] special consultant for that
  • QuickBooks Desktop Pro is a standard for small companies and makes it easy to hire bookkeepers
Read full review
ScreenShots

Paychex Screenshots

Screenshot of Screenshot of Screenshot of