Paychex Flex vs. QuickBooks Online

Overview
ProductRatingMost Used ByProduct SummaryStarting Price
Paychex Flex
Score 6.7 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 Online
Score 8.0 out of 10
N/A
QuickBooks Online is a SaaS version of the QuickBooks product. It contains all of the features found in the local version. Higher-priced plans include greater automation, payment management, inventory and time tracking, and analytics features.
$15
per month
Pricing
Paychex FlexQuickBooks Online
Editions & Modules
Paychex Go
$59
per month/+$4 per employee
Paychex Flex Service
Contact sales team
Paychex Flex Enterprise
Contact sales team
Self-Employed
$15
per month
Simple Start
$25
per month
Plus
$75
per month
Advanced
$150
per month
Offerings
Pricing Offerings
Paychex FlexQuickBooks Online
Free Trial
NoYes
Free/Freemium Version
NoNo
Premium Consulting/Integration Services
NoNo
Entry-level Setup FeeRequiredNo setup fee
Additional Details
More Pricing Information
Community Pulse
Paychex FlexQuickBooks Online
Considered Both Products
Paychex Flex
Chose Paychex Flex
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 Flex
Paychex Flex is hands-down an easier way to manage payroll. I found QuickBooks Online to be somewhat confusing about when and where to file what form, and it was definitely more tedious than the easy flow of using 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
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 Flex
Paychex more attentive to call backs for issues
Chose Paychex Flex
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 Flex
Better customer service; support with onboarding; employee self-service. Time savings.
Chose Paychex Flex
Moved from Heartland, too many processing issues and site crashes. Paychex Flex site is easy to use and we like the portal for the employees.
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
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 Flex
Actually, Paychex Flex is my first! I couldn't have asked for a better instructor!!
Thank you
Chose Paychex Flex
I have reviewed or used many other HRM and Payroll products. Paychex is a very solid program that overall does a very strong job. It is definitely competitive in the sense that it is constantly improving. With any large software system, there are glitches and issues that need …
Chose Paychex Flex
My accountants preferred a nationwide company.
Chose Paychex Flex
We evaluated an early time clock offering but the integration to flex was poor and it did not work well when employees worked in multiple tax jurisdictions in the same pay period. Paychex over sold and under delivered, so after the initial set up and test, we elected not to …
Chose Paychex Flex
Paychex is light years ahead. They are so much more client oriented and pleasant to work with. For about the same money I would pick Paychex every time.
Chose Paychex Flex
We previously used ADP and QuickBooks payroll. But I feel that the features that Paychex Flex offers benefits my payroll needs more.
Chose Paychex Flex
The ADP software is similar, but the customer service provided by Paychex is why they are better. I get answers from my Payroll Specialist in minutes, not days like ADP.
QuickBooks Online

No answer on this topic

Top Pros
Top Cons
Features
Paychex FlexQuickBooks Online
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 Online
-
Ratings
Employee demographic data8.0197 Ratings00 Ratings
Employment history8.0220 Ratings00 Ratings
Job profiles and administration6.8155 Ratings00 Ratings
Workflow for transfers, promotions, pay raises, etc.7.4154 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 Online
3.1
78 Ratings
83% below category average
Pay calculation9.0271 Ratings4.269 Ratings
Off-cycle/On-Demand payment9.1136 Ratings00 Ratings
Benefit plan administration7.3156 Ratings3.732 Ratings
Direct deposit files9.3270 Ratings4.765 Ratings
Salary revision and increment management8.5193 Ratings1.744 Ratings
Reimbursement management7.9105 Ratings1.446 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 Online
-
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 Online
-
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 Online
-
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 Online
-
Ratings
Report builder5.8134 Ratings00 Ratings
Pre-built reports6.9154 Ratings00 Ratings
Ability to combine HR data with external data5.783 Ratings00 Ratings
Onboarding
Comparison of Onboarding features of Product A and Product B
Paychex Flex
8.0
158 Ratings
0% below category average
QuickBooks Online
-
Ratings
New hire portal8.1151 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 Online
-
Ratings
Job Requisition Management9.632 Ratings00 Ratings
Company Website Posting9.730 Ratings00 Ratings
Publish to Social Media6.923 Ratings00 Ratings
Job Search Site Posting6.830 Ratings00 Ratings
Duplicate Candidate Prevention6.928 Ratings00 Ratings
Applicant Tracking9.633 Ratings00 Ratings
Notifications and Alerts9.753 Ratings00 Ratings
Customization
Comparison of Customization features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Online
2.6
68 Ratings
92% below category average
API for custom integration00 Ratings1.354 Ratings
Plug-ins00 Ratings3.857 Ratings
Security
Comparison of Security features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Online
3.7
108 Ratings
72% below category average
Single sign-on capability00 Ratings3.081 Ratings
Role-based user permissions00 Ratings4.5102 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Online
5.4
132 Ratings
34% below category average
Dashboards00 Ratings4.7124 Ratings
Standard reports00 Ratings5.4128 Ratings
Custom reports00 Ratings6.0116 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Online
3.8
143 Ratings
64% below category average
Accounts payable00 Ratings5.4122 Ratings
Accounts receivable00 Ratings6.0131 Ratings
Cash management00 Ratings6.2120 Ratings
Bank reconciliation00 Ratings6.3137 Ratings
Expense management00 Ratings5.5123 Ratings
Time tracking00 Ratings1.856 Ratings
Fixed asset management00 Ratings5.353 Ratings
Multi-currency support00 Ratings1.423 Ratings
Multi-division support00 Ratings1.542 Ratings
Regulations compliance00 Ratings1.738 Ratings
Electronic tax filing00 Ratings5.266 Ratings
Self-service portal00 Ratings2.666 Ratings
Global Financial Support00 Ratings1.416 Ratings
Primary and Secondary Ledgers00 Ratings3.535 Ratings
Intercompany Accounting00 Ratings5.029 Ratings
Localizations00 Ratings4.121 Ratings
Journals and Reconciliations00 Ratings5.274 Ratings
Enterprise Accounting00 Ratings1.825 Ratings
Configurable Accounting00 Ratings2.138 Ratings
Centralized Rules Framework00 Ratings2.924 Ratings
Standardized Processes00 Ratings4.048 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Online
1.3
47 Ratings
138% below category average
Inventory tracking00 Ratings1.345 Ratings
Automatic reordering00 Ratings1.222 Ratings
Location management00 Ratings1.321 Ratings
Manufacturing module00 Ratings1.317 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
Paychex Flex
-
Ratings
QuickBooks Online
3.7
86 Ratings
67% below category average
Pricing00 Ratings4.755 Ratings
Order entry00 Ratings4.753 Ratings
Credit card processing00 Ratings2.463 Ratings
Cost of goods sold00 Ratings3.968 Ratings
Order Orchestration00 Ratings4.621 Ratings
End-to-end order visibility00 Ratings4.620 Ratings
Order exception Resolution00 Ratings1.218 Ratings
Best Alternatives
Paychex FlexQuickBooks Online
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 8.2 out of 10
All AlternativesView all alternativesView all alternatives
User Ratings
Paychex FlexQuickBooks Online
Likelihood to Recommend
7.7
(298 ratings)
4.2
(161 ratings)
Likelihood to Renew
8.9
(42 ratings)
2.5
(24 ratings)
Usability
8.0
(240 ratings)
4.1
(76 ratings)
Availability
9.3
(10 ratings)
2.1
(5 ratings)
Performance
9.1
(10 ratings)
1.1
(4 ratings)
Support Rating
7.8
(245 ratings)
2.2
(68 ratings)
In-Person Training
4.5
(1 ratings)
-
(0 ratings)
Online Training
7.0
(4 ratings)
-
(0 ratings)
Implementation Rating
9.4
(11 ratings)
3.0
(6 ratings)
Configurability
7.6
(8 ratings)
10.0
(1 ratings)
Ease of integration
9.0
(3 ratings)
1.4
(2 ratings)
Product Scalability
9.3
(10 ratings)
1.1
(2 ratings)
Vendor post-sale
8.9
(31 ratings)
1.1
(2 ratings)
Vendor pre-sale
9.2
(32 ratings)
1.1
(2 ratings)
User Testimonials
Paychex FlexQuickBooks Online
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
It seems Intuit is more interested in generating revenue than taking care of their customers. After only 28 (working) days using it, I've had to call for Help 23 times, and, in my experience, only spoken to 2 people who had an understanding of basic accounting practices and the ramifications of some of their suggested fixes on the General Ledger.
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
  • It enables me to do a P&L for each specific program as requested by the county for the grant money that they give us.
  • It enables me to do [an] organizational budget as well as a budget for each specific program
  • It enables the accountant and the auditor access at any time for transparency
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
  • The budgets feature leaves a lot be desired - difficult and clunky to populate and maintain.
  • Reporting for Budget vs Actual is available but the ability to reforecast based on updated data is not.
  • The rules function to default common types of expenses isn't perfect and will get confused if like amounts or a number of similar items present.
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
It like the product 'right out of the box' and I trust Intuit will continually improve it over the years based on my experience with their desktop products. The large providers of Apps makes customizing the entire package relatively easy and seamless for a wide variety of business types.
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
While QuickBooks Online is generally easy to navigate, there are some features and functions that often require a Google search in order to find out where they are actually hidden. Additionally, there are some simple customization features that are surprisingly not available for an otherwise advanced program (e.g. only having a pool of 4 fonts to choose from, only having 4 very limited templates for invoicing, not color selection, etc). While I would say that about 75% of users shouldn't have a problem finding their way around with basic functions, there is a learning curve if you want to be able to dive into some of the more useful features, almost to the point that you need to have a dedicated account manager in order to use QuickBooks Online most effectively.
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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.
Read full review
Intuit
We have rarely had outages in the last 10 years. I can only recall 2 times in the last 10 years where we were not able to access our client files.
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
There are tab issues. When I tab the field doesn't highlight and I have to backspace or delete what is in the field. Happens on the memo field and sometimes other fields. Very time consuming.
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
Support is great, all incidents been resolved. Quickbooks Online forum is very well organized and helpful. I like the fact that they let the community contribute in resolving issues. Most or many of your answers can be found online. You can also get help on YouTube, but the easiest way to get assistance is through their chat system.
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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
The person in charge of QB needs to be very accurate with record keeping and is recommended to stay on top of tasks. The biggest issue we have is reconciliation, and those issues occur only when too much time has occurred between reconciliations
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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.
Read full review
Intuit
I have used Wave Accounting for another business. I selected QuickBooks Online over Wave because of the features available from QuickBooks. Wave is great since it is free, but I feel that paying for QuickBooks Online is worth it for the features. In addition there is such a robust support network and training available for QuickBooks.
Read full review
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.
Read full review
Intuit
As we have grown along our professional path, we have also expanded our use of QB. The scalability is easy and features seem to be waiting for you until you need them. We have increased profits by over 10x from our first year in business to the current and have yet to find a reason to look elsewhere
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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
  • It has created a lot of cost and in-efficiency whenever we need to talk to support.
  • I spent a lot of time setting up their automatic reminders for past due invoices and it worked for a couple of months and then it stopped. It's currently being worked on by their tech team but it has been months and it is still not working. It would have saved me a lot of time.
  • Their multi-currency saves time in sending invoices abroad but it's limiting when a customer wants an invoice in USD instead of a foreign currency so I have to set up different customer accounts for different currencies.
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ScreenShots

Paychex Flex Screenshots

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