Paychex vs. QuickBooks Online

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 Online
Score 8.2 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.
$38
per month
Pricing
PaychexQuickBooks Online
Editions & Modules
Paychex Go
$59
per month/+$4 per employee
Paychex Flex Service
Contact sales team
Paychex Flex Enterprise
Contact sales team
Simple Start
$38
per month
Essentials
$75
per month
Plus
$115
per month
Advanced
$275
per month
Offerings
Pricing Offerings
PaychexQuickBooks Online
Free Trial
NoYes
Free/Freemium Version
NoNo
Premium Consulting/Integration Services
NoYes
Entry-level Setup FeeRequiredNo setup fee
Additional Details
More Pricing Information
Community Pulse
PaychexQuickBooks Online
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
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
They were alright, some of the same issues. Lots of turnover with payroll consultants.
Chose Paychex
Both ADP and Paychex are very good at informing businesses of the latest changes regarding payroll. Not sure which one is better, but very much get the most out of each. Both are informative and always looking at additional topics in a world that is constantly changing. …
Chose Paychex
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
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 more attentive to call backs for issues
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
Better customer service; support with onboarding; employee self-service. Time savings.
Chose Paychex
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
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
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
Actually, Paychex Flex is my first! I couldn't have asked for a better instructor!!
Thank you
Chose Paychex
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
My accountants preferred a nationwide company.
Chose Paychex
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
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.
QuickBooks Online

No answer on this topic

Features
PaychexQuickBooks Online
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 Online
-
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 Online
7.9
108 Ratings
5% above category average
Pay calculation8.1292 Ratings8.298 Ratings
Off-cycle/On-Demand payment6.7150 Ratings00 Ratings
Benefit plan administration6.9171 Ratings7.251 Ratings
Direct deposit files8.3291 Ratings8.490 Ratings
Salary revision and increment management7.8207 Ratings8.064 Ratings
Reimbursement management7.7116 Ratings7.770 Ratings
Leave and Attendance Management
Comparison of Leave and Attendance Management features of Product A and Product B
Paychex
7.2
158 Ratings
13% below category average
QuickBooks Online
-
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 Online
-
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 history7.8181 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 Online
-
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 Online
-
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 Online
-
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 Online
-
Ratings
Job Requisition Management5.736 Ratings00 Ratings
Company Website Posting5.634 Ratings00 Ratings
Publish to Social Media4.928 Ratings00 Ratings
Job Search Site Posting5.335 Ratings00 Ratings
Duplicate Candidate Prevention5.134 Ratings00 Ratings
Applicant Tracking5.239 Ratings00 Ratings
Notifications and Alerts5.362 Ratings00 Ratings
Customization
Comparison of Customization features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
6.8
99 Ratings
13% below category average
API for custom integration00 Ratings6.781 Ratings
Plug-ins00 Ratings6.881 Ratings
Security
Comparison of Security features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
8.4
169 Ratings
2% above category average
Single sign-on capability00 Ratings8.5134 Ratings
Role-based user permissions00 Ratings8.2159 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
8.3
195 Ratings
6% above category average
Dashboards00 Ratings8.3182 Ratings
Standard reports00 Ratings8.6190 Ratings
Custom reports00 Ratings7.9173 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
7.8
212 Ratings
2% above category average
Accounts payable00 Ratings8.9179 Ratings
Accounts receivable00 Ratings8.8196 Ratings
Cash management00 Ratings8.2179 Ratings
Bank reconciliation00 Ratings9.0201 Ratings
Expense management00 Ratings8.4185 Ratings
Time tracking00 Ratings6.882 Ratings
Fixed asset management00 Ratings7.982 Ratings
Multi-currency support00 Ratings6.736 Ratings
Multi-division support00 Ratings7.464 Ratings
Regulations compliance00 Ratings7.664 Ratings
Electronic tax filing00 Ratings8.199 Ratings
Self-service portal00 Ratings7.4109 Ratings
Global Financial Support00 Ratings6.528 Ratings
Primary and Secondary Ledgers00 Ratings7.957 Ratings
Intercompany Accounting00 Ratings8.057 Ratings
Localizations00 Ratings7.742 Ratings
Journals and Reconciliations00 Ratings8.4126 Ratings
Enterprise Accounting00 Ratings6.847 Ratings
Configurable Accounting00 Ratings7.771 Ratings
Centralized Rules Framework00 Ratings7.546 Ratings
Standardized Processes00 Ratings8.789 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
6.6
75 Ratings
13% below category average
Inventory tracking00 Ratings6.470 Ratings
Automatic reordering00 Ratings7.037 Ratings
Location management00 Ratings7.041 Ratings
Manufacturing module00 Ratings6.127 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
7.5
127 Ratings
1% below category average
Pricing00 Ratings7.878 Ratings
Order entry00 Ratings7.574 Ratings
Credit card processing00 Ratings8.195 Ratings
Cost of goods sold00 Ratings8.295 Ratings
Order Orchestration00 Ratings6.736 Ratings
End-to-end order visibility00 Ratings7.639 Ratings
Order exception Resolution00 Ratings6.832 Ratings
Best Alternatives
PaychexQuickBooks Online
Small Businesses
Dayforce Powerpay
Dayforce Powerpay
Score 9.5 out of 10
QuickBooks Self-Employed (discontinued)
QuickBooks Self-Employed (discontinued)
Score 9.0 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 Online
Likelihood to Recommend
6.7
(323 ratings)
8.2
(230 ratings)
Likelihood to Renew
1.8
(44 ratings)
9.0
(27 ratings)
Usability
7.0
(264 ratings)
8.4
(145 ratings)
Availability
6.1
(12 ratings)
8.7
(6 ratings)
Performance
7.2
(12 ratings)
1.0
(5 ratings)
Support Rating
6.7
(265 ratings)
9.1
(70 ratings)
In-Person Training
4.5
(1 ratings)
-
(0 ratings)
Online Training
8.2
(4 ratings)
-
(0 ratings)
Implementation Rating
5.7
(13 ratings)
9.3
(7 ratings)
Configurability
5.2
(9 ratings)
1.0
(2 ratings)
Contract Terms and Pricing Model
-
(0 ratings)
5.0
(1 ratings)
Ease of integration
9.1
(3 ratings)
1.3
(2 ratings)
Product Scalability
6.7
(12 ratings)
2.0
(3 ratings)
Professional Services
-
(0 ratings)
5.0
(1 ratings)
Vendor post-sale
3.0
(33 ratings)
4.8
(3 ratings)
Vendor pre-sale
3.9
(34 ratings)
4.8
(3 ratings)
User Testimonials
PaychexQuickBooks Online
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
I appreciate the ability to auto-generate invoices for recurring transactions, which saves time, as well as the option to set up auto-generated transactions. The report option is super helpful when reviewing information, as you can click to view the details in the report without having to go back and forth.
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
  • Workflows for accounts payable invoice review are terrific.
  • Bill payment allows you to pay vendors online via ACH or check without having to write a physical check, which reduces admin time.
  • The cloud based login lends well to a remote or hybrid work environment for staff.
  • QuickBooks Online allows you to pre-configure vendors' general ledger expense accounts. This helps with general ledger coding accuracy and consistency.
  • QuickBooks Online integrates with Rippling HRIS, Coast, Capital One, JPMorgan Chase, etc., which lends well to an efficient month-end closing and reduced administrative time.
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
  • The upsells have gotten worse over time and are on every screen in the most awkward positions. I don't need a constant reminder to upgrade, especially on a very old account that's paid thousands over the years.
  • The interface has never been especially intuitive, but I was an old Quicken user and it was somewhat familiar. Over time, it's gotten worse, and in the last 2 years, the program seems to move things more often than I would expect.
  • The software constantly adds features that I don't want and want to turn off, but the interface is so difficult to use that I find myself skipping it. Imagine seeing a message that the system recognized invoices that hadn't been paid so it prepared reminder notices for you that can be sent at the click of a button. Who thinks using canned reminders that you've never seen is a good thing?
  • A lot of functionality seems to derive from connecting your bank accounts to QBO. I don't want Intuit to have an always-on connection to any bank accounts, even checking.
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
I had very little trouble setting up the program and migrating from our old accounting system. The daily usage is also very intuitive and easy. Anytime we run into minor trouble with the program, there are always tons of help available on YouTube, so we don't even look up the online manual anymore.
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
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.
Read full review
Intuit
Everything process has its bugs lately with the new interface. Nothing has worked smoothly since this all began last month.
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.
Read full review
Intuit
In my experience, most representatives keep me on the phone for hours, literally, for a single issue and then usually cannot resolve it satisfactorily. I have 10 open cases that need resolution and, in my experience, there has been NO follow-up communication on any of them.
Read full review
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.
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
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
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
As a freelance bookkeeper, the Desktop version of QuickBooks Online doesn't allow for ease of access from any device. Having to be on a computer with the software downloaded creates additional work to gain access to all required filings etc. Also, I personally find the linking functionality on the Online version to be much more streamlined and user friendly.
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
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
Read full review
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
  • QuickBooks has given us a useful portal by which to get an overview of our financials.
  • QuickBooks has given us a relatively easy way to send out invoices quickly and efficiently.
  • Due to the customization limitations on QuickBooks, we've had to get creative in third-party implementations to better represent our brand and to track financials.
Read full review
ScreenShots

Paychex Screenshots

Screenshot of Screenshot of Screenshot of

QuickBooks Online Screenshots

Screenshot of the accounting and bank transactions interfaceScreenshot of an overview of the accounting inventoryScreenshot of book marksScreenshot of the business tax overviewScreenshot of the customer hubScreenshot of the dashboard