Paychex vs. QuickBooks Online

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 Online
Score 8.1 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 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
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
6.7
272 Ratings
19% below category average
QuickBooks Online
-
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 Online
8.1
121 Ratings
7% above category average
Pay calculation8.0295 Ratings8.4110 Ratings
Off-cycle/On-Demand payment7.1153 Ratings00 Ratings
Benefit plan administration6.9174 Ratings7.260 Ratings
Direct deposit files8.3294 Ratings8.5101 Ratings
Salary revision and increment management8.0209 Ratings8.274 Ratings
Reimbursement management7.7118 Ratings7.981 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 Online
-
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 Online
-
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 Online
-
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 Online
-
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 Online
-
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 Online
-
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 Online
7.0
113 Ratings
8% below category average
API for custom integration00 Ratings7.194 Ratings
Plug-ins00 Ratings7.095 Ratings
Security
Comparison of Security features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
8.4
186 Ratings
2% above category average
Single sign-on capability00 Ratings8.5151 Ratings
Role-based user permissions00 Ratings8.3176 Ratings
Reporting & Analytics
Comparison of Reporting & Analytics features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
8.2
212 Ratings
5% above category average
Dashboards00 Ratings8.3199 Ratings
Standard reports00 Ratings8.4206 Ratings
Custom reports00 Ratings7.9190 Ratings
General Ledger and Configurable Accounting
Comparison of General Ledger and Configurable Accounting features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
8.0
229 Ratings
5% above category average
Accounts payable00 Ratings8.8195 Ratings
Accounts receivable00 Ratings8.8212 Ratings
Cash management00 Ratings8.1194 Ratings
Bank reconciliation00 Ratings9.0218 Ratings
Expense management00 Ratings8.4202 Ratings
Time tracking00 Ratings7.095 Ratings
Fixed asset management00 Ratings8.094 Ratings
Multi-currency support00 Ratings7.548 Ratings
Multi-division support00 Ratings7.379 Ratings
Regulations compliance00 Ratings7.978 Ratings
Electronic tax filing00 Ratings8.1113 Ratings
Self-service portal00 Ratings7.4124 Ratings
Global Financial Support00 Ratings6.840 Ratings
Primary and Secondary Ledgers00 Ratings8.170 Ratings
Intercompany Accounting00 Ratings7.970 Ratings
Localizations00 Ratings7.954 Ratings
Journals and Reconciliations00 Ratings8.5141 Ratings
Enterprise Accounting00 Ratings7.160 Ratings
Configurable Accounting00 Ratings7.986 Ratings
Centralized Rules Framework00 Ratings7.757 Ratings
Standardized Processes00 Ratings8.8105 Ratings
Inventory Management
Comparison of Inventory Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
6.9
88 Ratings
6% below category average
Inventory tracking00 Ratings6.783 Ratings
Automatic reordering00 Ratings7.146 Ratings
Location management00 Ratings7.353 Ratings
Manufacturing module00 Ratings6.636 Ratings
Order Management
Comparison of Order Management features of Product A and Product B
Paychex
-
Ratings
QuickBooks Online
7.9
141 Ratings
5% above category average
Pricing00 Ratings8.090 Ratings
Order entry00 Ratings7.886 Ratings
Credit card processing00 Ratings8.4109 Ratings
Cost of goods sold00 Ratings8.3107 Ratings
Order Orchestration00 Ratings7.446 Ratings
End-to-end order visibility00 Ratings7.949 Ratings
Order exception Resolution00 Ratings7.542 Ratings
Best Alternatives
PaychexQuickBooks Online
Small Businesses
Dayforce Powerpay
Dayforce Powerpay
Score 9.3 out of 10
QuickBooks Self-Employed (discontinued)
QuickBooks Self-Employed (discontinued)
Score 5.9 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
Oracle Fusion Cloud Enterprise Performance Management
Oracle Fusion Cloud Enterprise Performance Management
Score 7.5 out of 10
All AlternativesView all alternativesView all alternatives
User Ratings
PaychexQuickBooks Online
Likelihood to Recommend
6.2
(321 ratings)
8.3
(230 ratings)
Likelihood to Renew
1.2
(44 ratings)
9.5
(27 ratings)
Usability
6.7
(264 ratings)
8.3
(146 ratings)
Availability
5.5
(12 ratings)
9.0
(6 ratings)
Performance
7.1
(12 ratings)
1.0
(5 ratings)
Support Rating
6.1
(264 ratings)
9.8
(70 ratings)
In-Person Training
4.5
(1 ratings)
-
(0 ratings)
Online Training
8.3
(4 ratings)
-
(0 ratings)
Implementation Rating
5.3
(13 ratings)
9.9
(7 ratings)
Configurability
5.0
(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
5.9
(12 ratings)
2.0
(3 ratings)
Professional Services
-
(0 ratings)
5.0
(1 ratings)
Vendor post-sale
2.2
(33 ratings)
5.0
(3 ratings)
Vendor pre-sale
3.2
(34 ratings)
5.0
(3 ratings)
User Testimonials
PaychexQuickBooks Online
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
QBO is a great solution for small and midsize companies. If the goal is to record all transactions and pull reliable financial reports, QBO is a great option. QBO is also a great solution if most operations are run in a system like Ramp. It syncs well with systems like that and turns the data into something management can use to make decisions. QBO is great because so many people use it. It is easy to find training online, and many people have experience with it.
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.
  • 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
  • I dislike that the online bill pay option through QuickBooks is required for their invoicing.
  • The auto-fill portion of the customer setup, specifically the company name, is listed, but it also auto-fills in the name portion, which is inconvenient and time-consuming to remove.
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.
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
Beyond being overkill for a small org's needs, QBO is constantly stealing screen real estate and attention by hammering users for account upgrades, connecting to one of their approved consultants or buying add-ons. The idea of using a simple configurable bookeeping and light accounting interface is completely missing. At the very least, we should be able to hide functions like inventory that we will never use.
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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.
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.
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.
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.
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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.
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.
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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
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.
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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
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.
  • 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
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 Paychex Payroll DashboardScreenshot of Employee Background ChecksScreenshot of Paychex HR DashboardScreenshot of Paychex Flex Perks

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