Home > Payroll Software > Paychex Flex > Paychex Flex vs QuickBooks Payroll

Paychex Flex vs QuickBooks Payroll

Last Updated: November 18th, 2024

Our analysts compared Paychex Flex vs QuickBooks Payroll based on data from our 400+ point analysis of Payroll Software, user reviews and our own crowdsourced data from our free software selection platform.

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Product Basics

Paychex Flex is a cloud-based compensation and HR solution with the capability to serve thousands of employees. While there is an essential core version that mainly handles financials, it runs a wide range of departments and tasks. Some of its functions include payment management, benefits, talent management, time clocks, attendance, workforce management and more.

It’s a scalable option with unique versions for small, medium and large businesses with different versions for groups of varying sizes, including one to nine, 10 to 49, and 50 to thousands. It also has distinct user roles for workers, managers or administrators. A winner of multiple industry awards, its automation cuts down on time doing manual operations like processing payments, auto calculating taxes and staying up to date with current rates and compliance.

Quickbooks is an Intuit payroll and accounting solution designed to meet the needs of both small and medium-sized, growing businesses. There are a variety of plans, starting with small packages built for independent contractors and self-employed individuals. It handles payment, calculating and filing taxes, benefits management, direct deposits and more.

The variety of products and packages enables users to find a solution that fits a company’s unique needs. Quickbooks offers specialized features for organizations in a variety of fields, including manufacturing and retail. Overall, it serves 1.4 million businesses.

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Product Insights

Better Organization: Centralize important files and payroll data in one centralized location, making it easier to access. Assign user roles through administration; organizations control the dissemination of sensitive data.
Greater Accuracy: Run auto calculations for taxes and direct deposit and sync the general ledger making it easy to plug the information into an integrated accounting program. Creates a streamlined, easy way to manage all of the relevant data.
Increased Efficiency: Save time and work by decreasing the amount of manually input data. Record attendance within the application, making payment more straightforward. Auto-calculate local, state and federal taxes saving tons of manpower and time.
Better Scalability: Grow the platform as the company experiences exponential growth. Go from workplaces with as few as two employees to workforces that number in the thousands. Each level comes with more functionality and increased administrative and HR control over the processes.
More Open Communication: Use notifications, mass emails and electronic bulletin boards to promote an easy flow of information. Communicate enrollment reminders, announcements or company news seamlessly. Ensure employees, managers, executives, contractors, remote workers and other employees are all on the same page.

Save Time: Connects with bank accounts and syncs with various apps to help streamline payroll processing. Saves users more than 40 hours monthly on average and spares them from tedious manual data entry.
Save Money: Saves the average users more than $3,500 annually through its assistance with tax filing and other processes.
Easy-to-Use: Provides a simple interface so HR managers and others can store and access relevant accounting information easily. Centralizes and organizes data, making it simple to access.
Simplified Administration: Manages benefits, payments, time tracking, workers’ compensation, inventory, compliance and other essential business functions from one location. Simplifies processes and handles all of them through one solution.

Online Payroll: Handle payroll management. Automatically calculate taxes, payments and files. View critical data, including the cash required for upcoming paydays. Use safeguards such as notifications to prevent errors. Employees can access direct deposit and pay stub information directly. Last, administrators can access documentation and records like cash requirements, the payroll journal and tax deposit notices.
Tax Administration: Calculate taxes, add hours to each pay period, file returns and set up direct deposit.
Mobile: Access information on W-2s, direct deposit and other important information. For organizations that want to use the solution’s attendance functionality, workers can easily punch in and out on the app. Run it on smartphones and tablets with iOS or Android. It requires iOS 12.0 or higher and an Android OS of 7.0 or higher to run.
Reporting: Comes with over 160 dashboards and reports. Access reporting for payroll journals, department summaries, notices of tax deposits and cash requirements. For businesses looking for more robust options, look into the workforce management options.
Multiple Versions: Choose from a variety of purchase options to select the option that best meets business needs. The packages include:

Small Business Payroll: Use for businesses with under 50 workers. Use payment processing and access to the mobile app. Calculate state, federal and local taxes. Finish onboarding, complete forms, edit personal info and see compensation data. Provide direct deposit, pay cards and paper check for payment options. For businesses with multiple worker types, offer payment hourly, by salary or by contract. Provide help with labor compliance, garnishment payments, new hire reporting and over 160 reports for analytics.
Mid-Sized Business Payroll: Use for businesses with 10 to 49 employees. Handle applicant tracking, attendance, recruiting, onboarding, hiring, health benefits, retirement, health insurance and other similar administrative tasks. Expand the platform HR capabilities by including HR record management, an events calendar and reporting and analytics for the department.
Enterprise Payroll Management: Use for 50 to over 1,000 workers. Provide more robust HR abilities in addition to compensation management. Works for hiring, recruiting, training, compliance, handling offboarding, applicant tracking, time and attendance, health benefits, HR record management, an events calendar, retirement and expanded HR analytics.

Benefits: Complete the benefits management process. Run enrollment and analyze data. Manage group health insurance, retirement, section 125 plans, FSAs, POPs, retirement and more. Update information in real time and change benefit data easily. Give employers more control over invoices, benefit costs and bill reconciliations. Work with financial advisers and educate staff about the retirement plan offerings.
Compliance: Keep up with new tax laws and determine the status of essential laws like the Affordable Care Act.
Workplace Analytics: Analyze data and create a staff and workforce strategy. Create reports for analytics, HR, payroll and benefits. Generate customized reports for more detail. Provide accountants, financial advisors or bookkeepers with the access they need. Access the quick answers function, giving info on total earnings, net pay, tax liability and hours without pulling a full report. View live reporting to see information as it happens. Export information in various file types, including CSV, fixed-width, PDF and XLS. Send data to third-party software where users can add fields, adjust formatting or even build graphs.
Time and Attendance: Provide several options for tracking time and clocking in and out. It integrates with other solutions to track labor costs.

Time Kiosk: Allow employers to turn a tablet into a time clock where employees can punch in and out, do job transfer and register lunches and breaks.
TrueShift: Offer a time clock that has automated tracking and reporting, making it easy to import to payroll. Use biometric technology to prevent buddy punching. Track up to 500 workers per clock and connect to up to 32 other clocks. Punch in via web or mobile and use a backup camera to verify punches and keep compliant. It can track overtime pay and other wage requirements. Print and email timecard reports and clock in or out with a fingerprint, proximity badge, web punch or PIN entry.
InVision Iris Recognition Time Clock: Use iris recognition to ensure employees are working. Integrate with the rest of the HR and time and attendance. Prevent rework and cut down on errors. It works with contacts, goggles, glasses and face masks up to 15 inches away. Track up to 50,000 workers. Unlike a retinal scanner, it doesn’t store images. Instead, encrypt templates to guarantee privacy.

Online Learning: Use the built-in learning system. Provide eight free courses to users and customize/build current training, classes, quizzes and videos. Promote skill acquisition, up-skilling and career development. Run classes for on and offsite students. Use the calendar to schedule an in-person training, track transcripts and create content. Access the additional content libraries for purchase and provide surveys so employers can get feedback. Subjects include business, HR compliance, leadership, management, sales, software and workplace safety.
Payment Options: Gives options for paying employees, including same-day ACH capability, direct deposit, paper checks and pay cards.
Accounting: Manage payment and HR data with the accounting-specific dashboard. Access a library of resources, including tax forms and CPE courses. Import files through the general ledger service and post payroll data through the enterprise solution. Integrate with Sage Intacct, QuickBooks and Xero. Upload or download many files for one or multiple companies from one location.
Workers Compensation: Handle workers’ compensation covering medical expenses and lost wages while still ensuring stable cash flow. Provide insurance plans from A-rated national carriers.
Onboarding: Give new employees paperwork to fill out online. Customize the experience with personalized messages, welcome videos or other information about the company culture.
Payroll Protection: Let managers extend funds from a bank account for up to seven days without services being interrupted or charges for insufficient funds. Process two same-day ACH requests for a last-minute payroll, correcting pay or adding an employee. Help build business credit, deal with fraud, gain small business loans and more.

Payroll Processing: Operate 24-hour direct deposit. Pay employees, access integration services for employees, calculate taxes automatically and file taxes directly through the system. Automate payments to save time.
Benefits Management: Administrate workers’ compensation, health insurance, retirement plans and more. Covers workers’ compensation through AP Intego. Offers medical, dental and vision insurance through SimplyInsured. Compare different plans to judge the coverage, value and deductibles and make informed decisions. Calculates deductions for health, medical and dental automatically. Deducts and calculates contributions for 401(k)s from each employee paycheck.
Mobile Capabilities: Create, track and send invoices via smartphone as well as payment reminders.
Workers’ Compensation: Manage workers’ comp, understand state requirements and laws and pick a policy through AP Intego. Provides a free quote and automates premiums.
Inventory: Import information from Excel and sync with Amazon, Etsy and other similar websites to track products, cost of goods, create purchase orders and manage vendors.
HR Management and Compliance: Provides HR resources and consultation to help with compliance through Mammoth Inc. Creates forms from templates for onboarding checklists, employee handbooks and job descriptions. Aids in creating policies, obeying HR laws, hiring and conflict management.
Time Tracking: Track and add billable hours to invoices. Review and put a stamp of approval on employee timesheets. Provides tracking through TSheets. Link hours to specific jobs, save time during payment processing and see real-time insights into employee work hours. Approve and enter employee time cards.
Reporting: Run and export a variety of reports. Create customizable reports for balance sheets, expenses and tracking profit and loss. Create, export, print and customize reports to share with accountants or critical stakeholders. Covers deductions, tax liability, contributions, more than one worksite, summary for taxes and wages, vacation, workers’ compensation and sick leave.
Taxes: Helps users find tax deductions. Store photos of receipts, share books with accountants and sort business expenses by tax categories to help streamline tax filing.
Penalty Payments: Covers payments of up to $25,000 if errors in local, state or federal taxes result in a penalty. Communicates with the IRS. Reviews taxes with experts before sending them to the IRS to cut off issues before they start. Doesn’t cover specific penalties in some situations such as fraud, insufficient funds, healthcare administration, employee classification and several others.
Project Tracking: Track project details such as labor costs, expenses and profits.
Payroll Plans: Offers three separate plans for payroll needs.

Core: Provides core functionality such as payment and calculating payroll taxes.
Premium: Covers team management and provides more powerful tools and services for payroll.
Elite: Gives access to experts on-demand to answer payroll questions. Gives access to tax penalty protection.

Implementation: Aids in transferring current payroll information to the new system. Provides expert support to help users with initial setup and compliance.

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Analyst Rating Summary

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User Sentiment Summary

83%

of users recommend this product

Paychex Flex has a 'great' User Satisfaction Rating of 83% when considering 2205 user reviews from 4 recognized software review sites.

89%

of users recommend this product

QuickBooks Payroll has a 'great' User Satisfaction Rating of 89% when considering 626 user reviews from 4 recognized software review sites.

4.5 (24)

4.7 (17)

4.2 (1114)

4.0 (25)

4.1 (976)

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4.5 (550)

3.8 (91)

3.5 (34)

Awards

Synopsis of User Ratings and Reviews

User-Friendly: Just under 50% of reviews said the user experience was good and the interface worked well.

Good Support: Around 40% had good interactions with customer service and were happy with their level of care.

Proper Functionality: One-third of reviewers felt that the system was fully equipped with the tools they needed and especially liked the efficient payroll processing, benefits management, the transparency employees had on their payments and the PTO features.

Value for Price: Around 20% of reviews felt happy with the price and said it was well worth it.

Excellent Functionality: Over 90% of users that discussed functionality were happy with the features, including the tax filing, automation and employee salaries and hours functions.

Simple to Use: Reviewers that talked about the ease of use felt it had a simple and intuitive interface over 80% of the time.

Manage Salary and Hours: More than 80% who discussed the employee time tracking and salary functions felt it worked well.

Affordable: Just under 70% of users who discussed price felt it was an affordable option.

Issues with Features: Just under 40% of reviewers felt the features were lacking. The biggest concerns were that the UI was difficult to learn initially and the reporting wasn’t sophisticated enough.

Time and Attendance Systems: Over 20% of users had problems with the punching system or the biometric clocks.

Poor Customer Service: While users felt that the customer service was helpful overall, they noted a high rate of turnover with their reps which often led to gaps in service.

Bad for Large Organizations: Over 90% of reviewers that discussed using the system for big organizations felt the system wasn’t complex enough.

Mixed Customer Service: Users were split on customer support quality, with 52% approving and 48% disliking the service.

Issues with Price: While overall, reviewers that discussed price felt it affordable, over 30% were displeased and said they got overcharged or billed after they’d already canceled.

Paychex Flex is a solid payroll processing system best liked for its ease of use, positive customer service interactions, fair price and useful functionality. However, it comes with several drawbacks as well. While it’s easy to use, the onboarding takes time and can be initially frustrating. The customer service is good but the high turnover with representatives can be trying. A small but significant percentage had problems with the time and attendance features, either having issues with their punches not being registered or issues with the physical biometric clocks. Overall, it seems best for small and medium businesses looking to automate their payroll. Any organization with multiple types of workers, complex pay rules or many different kinds of income to report should be sure to demo the system carefully and may want to find a more complex option.

Quickbooks Payroll is part of the Intuit suite of programs. Commenters felt it was easy to use, train and adopt with a simple interface that worked well. They found it affordable and found the integrations of time tracking with employee salaries made running payroll a quick process. Commenters said it was reasonably priced and the features worked well. The most popular functionality included automation, tax calculations and filing, and its ability to centralize and organize data. The largest complaint by far was that this program isn’t complex enough for larger organizations. Reviewers recommended only using it for small organizations. Reactions to customer service were very mixed. Reviewers who were satisfied said the support workers got back to them quickly, were friendly, helpful and called back promptly. Other users had adverse reactions say the staff was incompetent, complaining that there was only chat support and complained of always getting different answers. While most were pleased with the price, some reported getting overcharged and said it was difficult to cancel with charges showing up well after they’d terminated the service. Quickbooks Payroll is a good choice for small and medium-sized businesses. Be sure to understand what functionality comes with which pricing plan before purchasing.

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FAQ

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