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Paychex Flex vs Aatrix

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

Overview Pricing Benefits & Features User Ratings Analyst Summary Screenshots
Paychex Flex Software Tool
Aatrix Software Tool
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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.
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Aatrix eFile is a cloud-based payroll software designed to streamline year-end tax reporting for businesses. It caters to businesses of all sizes, but its user-friendly interface and integrated filing system make it particularly attractive to those who lack dedicated HR personnel. Aatrix eFile boasts features like secure electronic filing of W-2s, 1099s, and ACA forms, directly from existing payroll software. Users can also choose to print and mail physical copies to employees. Aatrix eFile offers a cost-effective solution compared to traditional paper filing, with pricing based on the number of forms filed.
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$39 Monthly
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$25/User, Monthly
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Product Assistance

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FAQ
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Knowledge Base
24/7 Live Support
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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.
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  • Better Support: Learn the ins and outs of the service with extensive training and implementation support. Work with trained professionals to customize the processes to fit the needs of a business and its customers. 
  • Platform Separation: Focus on optimizing time and technical focus with Windows and Apple separation. Maximize the value of the software with specified implementation and support to save time and frustration.  
  • Simply Integration: Avoid switching between different apps and save time with one streamlined, convenient platform. Save time and prevent disconnects with one log-in hub for all platform functions. 
  • Simplified Filing: Avoid the end-of-year filing panic with continuous compliance throughout the calendar and fiscal year. 
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  • 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.
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  • Payment Processing: Simplify payment management with one platform for wage distribution, tracked hours, deductions, holidays and adjustments for PTO and sick leave. Automate clocking in and out with TimeCard and Top Pay integrations. 
  • Computerized Filing Services: File electronic employee, state and federal W2s and 1099s. Complete ACA filing, unemployment and new hire paperwork, 1095s and 1094-Bs and -Cs. Keep safe records of all file transactions. 
  • Traditional Paper Copies: Print any digital files to keep and paper trail and send to government agencies and recipients with nest-business day and selected delivery date options. 
  • AUF Compatability: Use the AUF (Aatrix Universal File) format to integrate payment processing data with any account or processing application. Translate AUF data with the built-in form viewer software to convert reports, view data and print. 
    • Integrated Filing: Communicate through the Single-Point eFile Center to send any payment reports to over 200 tax authorities for processing and filing for customers. 
  • Real-Time Tax Updates: Subscribe to the added tax table service to see changes to paychecks, employee compliance, deductions and duplications immediately reflected with automatic data updates. 
  • Populated Paperwork: Edit existing HR templates with appropriate company, employee and branding information to create performance reviews, disciplinary write-ups and employee handbooks. Finalized forms are stored in an encrypted company directory. 
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Product Ranking

#6

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Payroll Software

#78

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Payroll Software

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User Sentiment Summary

Great User Sentiment 2205 reviews
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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.

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4.5 (24)
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4.2 (1114)
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4.1 (976)
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3.8 (91)
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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.
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Saves Time: Streamlines payroll processes, automates calculations, and reduces manual data entry.
Improves Accuracy: Eliminates errors associated with manual payroll, ensuring timely and precise payments.
Enhances Compliance: Complies with complex tax regulations, reducing the risk of penalties and audits.
Increases Efficiency: Integrates with other business systems, such as HR and accounting, for seamless data flow.
Supports Employee Self-Service: Empowers employees with online access to pay stubs, tax forms, and other payroll-related information.
Cost-Effective: Affordable solution that provides significant savings compared to outsourcing or manual payroll processing.
Reliable and Secure: Backed by robust technology and industry-standard security measures, ensuring data protection.
Excellent Customer Support: Responsive and knowledgeable support team provides timely assistance and guidance.
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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.
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Complex User Interface: Users have reported difficulty navigating the software and finding the features they need, leading to frustration and reduced productivity.
Limited Reporting Capabilities: Aatrix offers limited reporting options, making it challenging for businesses to extract and analyze payroll data for decision-making.
Inaccurate Calculations: Users have experienced errors in payroll calculations, resulting in incorrect paychecks and potential legal issues.
Poor Customer Support: Aatrix has been criticized for slow response times and unhelpful customer support, leaving users with unresolved issues.
Outdated Technology: The software's interface and features feel outdated compared to competitors, making it less user-friendly and efficient.
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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.

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While not as widely reviewed as some competitors, Aatrix eFile garners positive feedback from users who praise its ease of use and affordability. A common theme is the straightforward interface, which reviewers often describe as intuitive – even for those without extensive payroll experience. This is particularly appealing to small businesses that might lack dedicated HR staff. However, some users found the W-2/1099 printing process trickier, requiring experimentation to ensure forms fit correctly in pre-printed envelopes. This can be frustrating, especially during busy tax filing seasons. Unlike some competitors, Aatrix eFile doesn't offer additional HR features like employee onboarding, which might be a drawback for businesses seeking a more comprehensive solution. Overall, Aatrix eFile seems best suited for small businesses or those with simple payroll needs. Its user-friendly design and affordable, per-form pricing make it a strong option for companies that prioritize cost-effectiveness and a streamlined year-end filing process. For businesses needing more robust HR functionalities or encountering printing difficulties, exploring alternative solutions might be worthwhile.

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