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    Overview
    ProductRatingMost Used ByProduct SummaryStarting Price

    Paychex

    Score6.9 out of 10
    N/APaychex 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 Pro

    Score7.8 out of 10
    N/AQuickbooks 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 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 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 Inc.
    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 …
    Incentivized
    Chose Paychex
    N/A
    Incentivized
    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 …
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    Chose Paychex
    Paychex has dedicated customer service
    Incentivized
    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. …
    Incentivized
    Chose Paychex
    Paychex Flex is always up to date and user friendly.
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    Chose Paychex
    Paychecx Flex is much more Affordable and efficient. Hard to choose any other company when using Paychex is a breeze.
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    Intuit
    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 …
    Incentivized
    Key User Insights
    Would buy again
    88%
    Would buy again
    267 Answers
    88%
    Would buy again
    29 Answers
    Delivers good value for the price
    90%
    Delivers good value for the price
    240 Answers
    93%
    Delivers good value for the price
    28 Answers
    Happy with the feature set
    93%
    Happy with the feature set
    281 Answers
    97%
    Happy with the feature set
    32 Answers
    Lived up to sales and marketing promises
    89%
    Lived up to sales and marketing promises
    202 Answers
    83%
    Lived up to sales and marketing promises
    20 Answers
    Implementation went as expected
    89%
    Implementation went as expected
    216 Answers
    96%
    Implementation went as expected
    25 Answers
    Features
    PaychexQuickBooks Desktop Pro
    Human Resource Management
    Comparison of Human Resource Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    7.3
    278 Ratings
    12% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    Employee demographic data7.7225 Ratings00 Ratings
    Employment history7.9248 Ratings00 Ratings
    Job profiles and administration7.7182 Ratings00 Ratings
    Workflow for transfers, promotions, pay raises, etc.7.8179 Ratings00 Ratings
    Organizational charting6.34 Ratings00 Ratings
    Organization and location management7.1163 Ratings00 Ratings
    Compliance data (COBRA, OSHA, etc.)6.4148 Ratings00 Ratings
    Payroll Management
    Comparison of Payroll Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    7.7
    319 Ratings
    6% below category average
    QuickBooks Desktop Pro
    6.7
    69 Ratings
    12% below category average
    Pay calculation8.0301 Ratings6.364 Ratings
    Support for external payroll vendors7.44 Ratings00 Ratings
    Off-cycle/On-Demand payment7.4157 Ratings00 Ratings
    Benefit plan administration7.2179 Ratings6.338 Ratings
    Direct deposit files8.3299 Ratings6.656 Ratings
    Salary revision and increment management8.0214 Ratings6.352 Ratings
    Reimbursement management7.4122 Ratings7.754 Ratings
    Leave and Attendance Management
    Comparison of Leave and Attendance Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    7.2
    161 Ratings
    13% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    Approval workflow7.5115 Ratings00 Ratings
    Balance details7.6153 Ratings00 Ratings
    Annual carry-forward and encashment6.4120 Ratings00 Ratings
    Employee Self Service
    Comparison of Employee Self Service features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    7.4
    276 Ratings
    11% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    View and generate pay and benefit information8.0254 Ratings00 Ratings
    Update personal information7.6266 Ratings00 Ratings
    View company policy documentation7.4125 Ratings00 Ratings
    Employee recognition6.33 Ratings00 Ratings
    View job history7.6190 Ratings00 Ratings
    Asset Management
    Comparison of Asset Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    6.3
    44 Ratings
    24% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    Tracking of all physical assets6.344 Ratings00 Ratings
    HR Reporting
    Comparison of HR Reporting features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    6.1
    179 Ratings
    22% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    Report builder6.5149 Ratings00 Ratings
    Pre-built reports6.8167 Ratings00 Ratings
    Ability to combine HR data with external data5.093 Ratings00 Ratings
    Onboarding
    Comparison of Onboarding features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    6.8
    176 Ratings
    17% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    New hire portal7.0168 Ratings00 Ratings
    Manager tracking tools6.7112 Ratings00 Ratings
    Performance and Goals
    Comparison of Performance and Goals features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    9.0
    1 Ratings
    10% above category average
    QuickBooks Desktop Pro
    -
    Ratings
    Corporate goal setting8.01 Ratings00 Ratings
    Individual goal setting9.01 Ratings00 Ratings
    Line-of sight-visibility9.01 Ratings00 Ratings
    Performance tracking10.01 Ratings00 Ratings
    Performance Management
    Comparison of Performance Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    9.0
    1 Ratings
    12% above category average
    QuickBooks Desktop Pro
    -
    Ratings
    Performance plans9.01 Ratings00 Ratings
    Performance improvement plans9.01 Ratings00 Ratings
    Review status tracking9.01 Ratings00 Ratings
    Review reminders9.01 Ratings00 Ratings
    Multiple review frequency9.01 Ratings00 Ratings
    Succession Planning
    Comparison of Succession Planning features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    7.7
    2 Ratings
    2% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    Candidate ranking7.31 Ratings00 Ratings
    Candidate search7.52 Ratings00 Ratings
    Candidate development8.21 Ratings00 Ratings
    Recruiting / ATS
    Comparison of Recruiting / ATS features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    5.3
    72 Ratings
    40% below category average
    QuickBooks Desktop Pro
    -
    Ratings
    Job Requisition Management5.138 Ratings00 Ratings
    Company Website Posting5.235 Ratings00 Ratings
    Publish to Social Media5.729 Ratings00 Ratings
    Job Search Site Posting6.037 Ratings00 Ratings
    Duplicate Candidate Prevention4.635 Ratings00 Ratings
    Applicant Tracking4.741 Ratings00 Ratings
    Notifications and Alerts6.266 Ratings00 Ratings
    Customization
    Comparison of Customization features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    -
    Ratings
    QuickBooks Desktop Pro
    5.7
    43 Ratings
    28% below category average
    API for custom integration00 Ratings6.535 Ratings
    Plug-ins00 Ratings5.039 Ratings
    Security
    Comparison of Security features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    -
    Ratings
    QuickBooks Desktop Pro
    8.4
    101 Ratings
    3% above category average
    Single sign-on capability00 Ratings8.382 Ratings
    Role-based user permissions00 Ratings8.595 Ratings
    Reporting & Analytics
    Comparison of Reporting & Analytics features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    -
    Ratings
    QuickBooks Desktop Pro
    8.5
    117 Ratings
    9% above category average
    Dashboards00 Ratings8.4100 Ratings
    Standard reports00 Ratings8.9117 Ratings
    Custom reports00 Ratings8.2114 Ratings
    General Ledger and Configurable Accounting
    Comparison of General Ledger and Configurable Accounting features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    -
    Ratings
    QuickBooks Desktop Pro
    7.5
    124 Ratings
    2% below category average
    Accounts payable00 Ratings9.3119 Ratings
    Accounts receivable00 Ratings9.2121 Ratings
    Cash management00 Ratings9.2107 Ratings
    Bank reconciliation00 Ratings9.7119 Ratings
    Expense management00 Ratings9.4108 Ratings
    Time tracking00 Ratings7.451 Ratings
    Fixed asset management00 Ratings5.669 Ratings
    Multi-currency support00 Ratings6.931 Ratings
    Multi-division support00 Ratings8.958 Ratings
    Regulations compliance00 Ratings8.342 Ratings
    Electronic tax filing00 Ratings8.355 Ratings
    Self-service portal00 Ratings5.941 Ratings
    Global Financial Support00 Ratings4.217 Ratings
    Primary and Secondary Ledgers00 Ratings7.140 Ratings
    Intercompany Accounting00 Ratings7.943 Ratings
    Localizations00 Ratings4.219 Ratings
    Journals and Reconciliations00 Ratings8.876 Ratings
    Enterprise Accounting00 Ratings6.838 Ratings
    Configurable Accounting00 Ratings7.647 Ratings
    Centralized Rules Framework00 Ratings5.427 Ratings
    Standardized Processes00 Ratings8.555 Ratings
    Inventory Management
    Comparison of Inventory Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    -
    Ratings
    QuickBooks Desktop Pro
    5.8
    59 Ratings
    23% below category average
    Inventory tracking00 Ratings6.056 Ratings
    Automatic reordering00 Ratings6.035 Ratings
    Location management00 Ratings6.032 Ratings
    Manufacturing module00 Ratings5.218 Ratings
    Order Management
    Comparison of Order Management features of Paychex and QuickBooks Desktop Pro
    Feature
    Paychex
    -
    Ratings
    QuickBooks Desktop Pro
    6.8
    77 Ratings
    8% below category average
    Pricing00 Ratings7.555 Ratings
    Order entry00 Ratings8.555 Ratings
    Credit card processing00 Ratings7.251 Ratings
    Cost of goods sold00 Ratings8.063 Ratings
    Order Orchestration00 Ratings5.220 Ratings
    End-to-end order visibility00 Ratings6.123 Ratings
    Order exception Resolution00 Ratings5.218 Ratings
    Best Alternatives
    PaychexQuickBooks Desktop Pro
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    UZIO
    Score9.4 out of 10
    QuickBooks Self-Employed (discontinued)
    Score4.3 out of 10
    Medium-sized Companies
    Zoho People
    Score8.6 out of 10
    MYOB
    Score8.3 out of 10
    Enterprises
    PeopleStrong
    Score10 out of 10
    Microsoft Dynamics GP
    Score5.3 out of 10
    All AlternativesView all alternativesView all alternatives
    User Ratings
    PaychexQuickBooks Desktop Pro
    Likelihood to Recommend
    6.8
    (334 ratings)
    8.5
    (135 ratings)
    Likelihood to Renew
    7.1
    (48 ratings)
    8.0
    (19 ratings)
    Usability
    7.2
    (275 ratings)
    9.1
    (42 ratings)
    Availability
    5.2
    (12 ratings)
    8.3
    (2 ratings)
    Performance
    7.0
    (12 ratings)
    -
    (0 ratings)
    Support Rating
    6.5
    (274 ratings)
    1.2
    (29 ratings)
    In-Person Training
    4.5
    (1 ratings)
    10.0
    (1 ratings)
    Online Training
    2.7
    (4 ratings)
    -
    (0 ratings)
    Implementation Rating
    5.1
    (13 ratings)
    9.0
    (6 ratings)
    Configurability
    5.0
    (9 ratings)
    -
    (0 ratings)
    CPA Rating
    -
    (0 ratings)
    8.5
    (22 ratings)
    Ease of integration
    9.1
    (3 ratings)
    -
    (0 ratings)
    Product Scalability
    5.4
    (12 ratings)
    8.0
    (1 ratings)
    Vendor post-sale
    5.7
    (34 ratings)
    -
    (0 ratings)
    Vendor pre-sale
    6.2
    (35 ratings)
    -
    (0 ratings)
    User Testimonials
    PaychexQuickBooks Desktop Pro
    Likelihood to Recommend
    Paychex Inc.
    It is best suited for payrolls from 1 to 150 employees, because their constant attention and flex system are easy to use. Any problem is taking care by your Paychex Agent, and they always listen to you. Better yet, when you become a client with more than 5 years, you get special discount on your renewal. Honestly, I can't not think on nothing that will be less appropriate.
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    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
    Incentivized
    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.
    Incentivized
    Read full review
    Usability
    Paychex Inc.
    Once you are set up in the system, it is very user-friendly and usability is on par with my expectations. Onboarding new employees is simple, employee access is simple and easy for them to use. Tax documentation, reporting, and entering payroll is easy and user-friendly. Running reports and finding information necessary to keep the flow moving foward is easy to do
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
    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
    Incentivized
    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.
    Incentivized
    Read full review
    Intuit
    No answers on this topic
    Support Rating
    Paychex Inc.
    The dedicated support we are given is good and very responsive. If there is a change to the dedicated support, we are notified quickly and have temporary support in place while we wait for our new rep. The phone support is knowledgeable and quick to help if there is an immediate need. However, the chat support can be the slowest option and doesn't always launch so I rarely use it.
    Incentivized
    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.
    Incentivized
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    In-Person Training
    Paychex Inc.
    We did online training only
    Incentivized
    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.
    Incentivized
    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.
    Incentivized
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    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.
    Incentivized
    Read full review
    Alternatives Considered
    Paychex Inc.
    In addition to the ones listed above, we also used BenePay, a local payroll company. We found Paychex Flex priced in the middle, with ADP the most expensive and too complicated, with many features that were unnecessary for us. We found that Paychex Flex's features and reporting to be sized right for our size (around 30 employees). Paychex Flex also offered a very reasonable service to apply for the ERTC
    Incentivized
    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.
    Incentivized
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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
    Incentivized
    Read full review
    Intuit
    No answers on this topic
    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
    Incentivized
    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
    Incentivized
    Read full review
    ScreenShots

    Paychex Screenshots

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