QuickBooks Online Payroll and Paychex Flex are both top choices for small-business owners managing payroll online. Paychex Flex is however notable for its dedicated payroll specialist and diverse payment options. On the other hand, QuickBooks Online Payroll distinguishes itself with health benefits administration and, in its premium plan, tax penalty protection.

Paychex Advantages

Multiple Payment Methods

What sets Paychex apart is its flexibility in employee payment options. You can pay employees through:

• Direct deposit: Funds are transferred directly into their personal bank accounts.
• Prepaid paycard: Employees receive their wages on a prepaid card.

If these options aren’t suitable, Paychex also offers paper checks. You can pay employees via paper checks, with the added features of check signing and custom check logos to personalize them for your business. While not every business may require these features, they are particularly valuable for those who do.

Payroll specialist

Regardless of the Paychex payroll plan you choose, you’ll have access to a dedicated payroll specialist. This is particularly beneficial for small businesses that may not have an HR specialist on staff. Unlike QuickBooks, which provides this support only with its higher-tier plans, Paychex includes a payroll specialist with every plan. Your specialist can assist with any payroll or tax questions, helping you avoid costly mistakes and ensuring smooth payroll management.

Paychex Plans

Depending on your business requirements, Paychex likely offers a plan tailored to your needs. With a range of options for various business sizes and needs, Paychex provides customized solutions. Note that pricing for each plan is provided on a quote basis.

Flex Select

The Paychex Flex Select plan is tailored for small businesses with less than 50 employees seeking comprehensive payroll software. It includes the following features:

• Payroll tax administration: Paychex Flex Select handles all your payroll taxes at the local, state, and federal levels, ensuring they are filed and paid on your behalf, so you can avoid the hassle of managing this yourself.
• New-hire reporting: Paychex Flex Select handles reporting for new hires and contractors according to your state’s regulations.
• Direct deposit and/or paycards: Pay employees through direct deposit or prepaid paycards.
• Employee and income verification services: Automated services for confirming employment and income information.
• Additional employee pay options: Besides direct deposit and paycards, you can also pay employees via paper check or check signing.
• Employee financial wellness: Provide your employees with access to educational tools for making informed financial decisions.
• Labor law poster kit: Receive a kit with state and federal worker information to display in your workplace for compliance.
• Free mobile app: Access the Paychex Flex app to manage payroll from your phone, allowing you to run payroll from anywhere.

Flex Pro

The Paychex Flex Pro plan is ideal for businesses with 50 or more employees. In addition to all the features of the Select plan, the Flex Pro plan includes the following additional features:

• General ledger: Link your accounting software with Paychex if you use QuickBooks Online, Xero, or Sage Intacct.
• Workers’ compensation report: Access detailed reports on wages subject to workers’ compensation and premium information.
• Garnishment payment: Automate the deduction and payment of garnished wages.
• State unemployment insurance: Assistance with managing unemployment insurance for your employees.
• Analytics and reporting: Over 160 customizable reports to provide insights into your business.
• Onboarding essentials: Enable new employees to complete tax forms and set up direct deposit online during onboarding.
• Screening essentials: Includes a limited number of background checks for new hires.

Enterprise

For businesses with 100 or more employees, the Paychex Flex Enterprise plan is the right choice. It includes all the features of the Select and Pro plans, with additional benefits such as:

• Customizable reporting: Advanced reporting options tailored to your specific business needs.
• HR administration: Develop a structured system for employee feedback and development, including schedule creation and training, all managed and stored securely in the cloud.

Paychex Cost

Paychex payroll plans use quote-based pricing, which means costs are not clearly listed upfront. This can make it challenging to compare Paychex directly with QuickBooks Online Payroll. Additionally, the lack of transparent pricing may be viewed as a downside for those seeking clear and straightforward cost information.

QuickBooks Payroll Advantages

Health Benefits Administration and Deduction

If you’re seeking payroll software with additional capabilities, QuickBooks might be a good fit. It offers health benefits administration and deductions, features typically found in HR management software. This integration can help you avoid the added cost of a separate HR system alongside your payroll software.

Tax Penalty Protection

Tax penalty protection is available only with QuickBooks’ most expensive plan, but it can be invaluable if your payroll taxes are complex. With this plan, QuickBooks will cover all penalty fees and interest up to $25,000 per year if you receive a tax penalty from the IRS. Their Tax Resolution Team will also represent you to resolve any issues promptly. If you do receive an IRS penalty, you must forward it to QuickBooks within 15 days to take advantage of this coverage.

QuickBooks Payroll Plans

QuickBooks, a leading name in business software owned by Intuit, offers three versions of its payroll software to cater to different business needs. Each version provides varying features to match your requirements.

Core

The QuickBooks Payroll Core plan is priced at $45 per month, plus $4 per employee per month. This plan includes the following features:

• Unlimited payroll runs: View, approve, or run payroll automatically for salaried employees, and easily adjust for bonuses or additional compensation.
• Payroll reports: Generate reports on payroll history, bank transactions, PTO statistics, and tax payments.
• Next-day deposit: Submit payroll by 8 p.m. ET to ensure employees receive their deposits the following day.
• Tax filing: State and federal taxes are calculated and filed on your behalf at the end of the year.
• Tax deductions: Automatic calculation and adjustment of taxes and other deductions from paychecks.
• Health benefits administration: Manage employee health benefits through the QuickBooks payroll portal.
• Workforce portal: Employees can access their W-2s, deductions, and PTO allowances online.

Premium

If you upgrade to the QuickBooks Payroll Premium plan, the cost is $75 per month plus $8 per employee per month. This plan includes all the features of the Core plan, with the following additional benefits:

• Same-day direct deposits: Run payroll and make deposits within the same day, eliminating the one-day wait.
• Workers’ comp administration: Receive quotes from QuickBooks’ broker, AP Intego, to compare pricing and plans for workers’ compensation.
• HR support center: Access expert HR support from Mammoth for guidance on state and federal overtime laws, hiring, firing, and onboarding.
• Time tracking on the go: Use GPS to track employee locations, and allow employees to clock in and out from anywhere with the TSheets mobile app integration.
• Expert setup: An expert will review your payroll setup to ensure everything is completed correctly.

Elite

The QuickBooks Payroll Elite plan, priced at $125 per month plus $10 per employee per month, offers all the features of the Core and Premium plans, with the following additional benefits:

• Time and project tracking: Effortlessly track expenses and hours on the go to avoid falling behind.
• Tax penalty protection: Coverage for IRS penalties due to QuickBooks filing errors, up to $25,000 annually, including interest. QuickBooks will also handle representation to resolve any issues.
• Personal HR advisor: Work with a personal HR advisor from Mammoth for assistance with custom handbooks, policies, and general HR guidance, available by phone or online.
• 24/7 expert product support: Support experts based in the U.S. are available anytime, with the added convenience of receiving calls directly instead of waiting on hold.
• Customized setup: A QuickBooks expert will ensure your payroll system is set up correctly from the start.

Exclusive Offer: 1 Month Free Payroll

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Verdict

Following a comprehensive evaluation, we’ve concluded that Paychex provides greater value and a wider range of services. By choosing Paychex, you’ll benefit from cost savings and enhanced HR support. While QuickBooks excels in offering employee benefits, we believe Paychex delivers a superior overall experience.