Top Payroll Software that Integrates with QuickBooks Online in 2025

Payroll management is important to businesses of any size, and finding the right payroll software can considerably affect how your operation runs. If your accounting platform is QuickBooks Online, working with Payroll That Integrates with QuickBooks will make that process easier and reduce much of the manual work involved with compliance regarding tax regulations.

Payroll management is what makes any company, big or small, successful. Right?

QuickBooks integrations are innovative for small business owners because they extend the capabilities of Intuit’s popular accounting program. These integrations go beyond making bookkeeping easier; they enhance coherence and productivity in workflow, smoothing many corporate operations like payroll, payments, invoicing, and cost management.

Here’s why integrating payroll software with QuickBooks can be a smart move for your business:

• Effortless data synchronization across platforms ensures a smooth flow of information between systems.
• Reduced manual errors by automating repetitive tasks and removing the need for manual data entry.
• Smarter project and client management with unified data that empowers superior oversight and decision-making.
• Holistic business insights, because integrated tools give you a clearer, more accurate picture of the performance of your business.

For both new users and longtime QuickBooks enthusiasts, the right integrations can transform how you manage your business.

Below, we review the top 5 Payroll solutions that work seamlessly with QuickBooks Online, helping you improve your payroll management and overall operations.

1) Gusto Payroll

Gusto is an end-to-end payroll and HR solution for simplifying employee management, and automating payroll processing to keep calculations, tax filings, and even payments at the federal, state, and local levels hassle-free, while making sure businesses remain compliant with continuously changing regulations.

Beyond payroll, Gusto has powerful tools to handle employee benefits, including health insurance and 401(k) retirement plans, to make offering competitive perks a whole lot easier. Gusto easily integrates with popular accounting software like QuickBooks and Xero, giving businesses a way to keep their financial records more accurate without dealing with duplicate data entry. In one neat bundle, Gusto is ideal for those businesses that need an easy-to-use online platform that bundles payroll, benefits administration, and HR functionality in one convenient location.

Gusto Payroll Features

• Automated Payroll: Automatically runs payroll, calculates taxes, and handles direct deposits.
• Benefits Management: Offers health insurance, 401(k) plans, and other employee benefits in one platform.
• Tax Filing: Gusto automatically files federal, state, and local payroll taxes for you.
• Employee Onboarding: Simplifies new employee setup with electronic forms, direct deposit, and offer letters.
• Time Tracking: Employees can log hours, and managers can approve timesheets for accurate payroll processing.
• Compliance Support: Ensures compliance with labor laws and tax regulations, including generating W-2s and 1099s.
• Integrations: Seamlessly integrates with popular tools like QuickBooks, Xero, and time-tracking apps.

Pros and Cons of Gusto Payroll:

Gusto Review from G2

Gusto Payroll Pricing and Plans

Why Custom Gusto Integration with QuickBooks Solutions Are Needed:

A custom Gusto integration with QuickBooks is tailored to meet the unique needs of businesses, offering more flexibility and control over how payroll and accounting systems interact. Unlike standard integrations, a custom solution ensures that specific workflows, business rules, and data management needs are addressed.

2) QuickBooks Payroll

QuickBooks Payroll is a comprehensive payroll solution designed to streamline payroll management for small to medium-sized businesses. It offers full-service payroll with features like automated tax calculations, payments, and filings, helping businesses ensure tax compliance.

With options for next-day or same-day direct deposit, it simplifies employee payments, while also integrating employee benefits like health insurance and 401(k) plans. The software integrates seamlessly with QuickBooks Online, providing businesses with a unified platform for both payroll and accounting.

QuickBooks Payroll is user-friendly and mobile-accessible, making it convenient for business owners, with customizable plans that cater to various business needs, from self-service to full-service options.

QuickBooks Payroll Features:

• Automated Payroll: Runs payroll automatically with scheduled payments and updates, reducing manual tasks.
• Tax Compliance: Calculates, files, and pays federal, state, and local taxes automatically, ensuring compliance.
• Direct Deposit: Offers next-day and same-day direct deposit options for quick employee payments.
• Employee Benefits: Integrates with health insurance, retirement plans, and other benefits for easy management.
• Time Tracking: Syncs employee hours through integration with QuickBooks Time (formerly TSheets) for accurate payroll.
• Customizable Payroll Plans: Offers flexible plans that scale with the business, from self-service to full-service payroll.
• Mobile Access: Allows users to run payroll and manage tasks on the go through the mobile app.

QuickBooks Payroll: Pros & Cons

QuickBooks Payroll Pricing and Plans:

Why QuickBooks Payroll May Need Custom Integration with QuickBooks

Although QuickBooks Payroll integrates natively with QuickBooks, certain businesses may encounter limitations in the standard integration that make custom integration essential. Here are the primary reasons why a custom integration might be needed:

Unique Payroll Processes, Compatibility with Non-Standard Workflows, Advanced Reporting Needs, Multiple Systems Involved, Handling High Transaction Volumes, Localization and Tax Compliance.

3) Paychex Flex

Paychex Flex is a simple employee payroll platform for small businesses, offered as an alternative to the more complex Paychex platform for larger businesses. It provides just what small businesses need: easy employee payroll.

Beyond that, the platform’s offerings are pretty slim compared with Paychex’s competitors—though Paychex as a whole offers a suite of integrated products you could purchase to meet your needs under one brand.

Paychex Flex Features:

Ease of Use: Simple for small businesses, but pricing is complex with customizable plans.

Compliance: Ensures state and local tax filing, includes new hire reporting, and provides labor law posters.

Tax Filing: Automatically calculates, pays, and files payroll taxes.

Time Tracking: Not included, but can be added through Paychex Flex Time with mobile app or kiosk.

Analytics and Reporting: Custom analytics and reporting available in Pro plan; basic plans lack reports.

Payroll: Runs payroll and processes payments via direct deposit or printed checks.

Pay Contractors: Pays contractors via direct deposit or printed checks; contractors access pay info via the portal.

Time Tracking (Add-on): Paychex Flex Time tracks attendance, mileage, and hours; additional cost for this feature.

Taxes and Compliance: Automatic tax calculations, filing, and access to labor compliance posters.

Paychex Flex: Pros & Cons

Paychex Flex Pricing Plans

Why Paychex Flex Payroll Software May Need Custom Integration with QuickBooks

Paychex Flex is a powerful payroll software that supports businesses with payroll processing, tax management, and employee benefits. However, businesses with unique workflows or advanced reporting needs may find limitations in the standard integration between Paychex Flex and QuickBooks. A custom integration bridges these gaps, offering tailored solutions for better financial management.

Advanced-Data Mapping, Multi-System Compatibility, Real-Time Data Synchronization, Handling Complex Payroll Structures, Advanced Reporting and Analytics, Industry-Specific Requirements.

4)ADP WorkForce Now

ADP Workforce Now is an all-in-one human capital management (HCM) solution designed for businesses of all sizes. It offers a wide range of tools to manage payroll, benefits, talent, and HR processes, all in a single platform.

The software helps businesses automate routine tasks like payroll processing and tax filing, while also offering advanced features such as employee self-service, compliance tracking, and workforce analytics.

It integrates seamlessly with various third-party apps and provides robust reporting capabilities to help companies make informed HR decisions. ADP Workforce Now is highly customizable and scalable, making it ideal for businesses looking to streamline their HR and payroll functions as they grow.

ADP WorkForce Now Features & Benefits:

• Payroll Management: Automates payroll processing, tax calculations, and filings.
• HR Management: Offers comprehensive tools for employee data management, benefits, and onboarding.
• Time and Attendance: Tracks employee hours and integrates with payroll for accurate calculations.
• Benefits Administration: Manages employee benefits like health insurance, 401(k), and other perks.
• Talent Management: Includes tools for recruiting, performance reviews, and employee development.
• Custom Reporting: Provides advanced reporting features for workforce analytics and business insights.

Pricing: Not Found in the application. For that, you need to get pricing according to their needs.

Account: Free trial is not available, you need to have an account.

ADP QuickBooks Integration: Yes, you can do a custom integration with QBO with the “Run Powered ADP”.

5) Rippling Payroll

Rippling is a unified platform that combines HR, IT, and payroll management in one system, making it a comprehensive solution for businesses. With Rippling QuickBooks integration, It automates and streamlines various administrative tasks. Like payroll processing, benefits administration, time tracking, and employee onboarding.

Additionally, Rippling stands out by managing both employee devices and apps alongside HR tasks, offering seamless integration with third-party software.

This all-in-one system is highly customizable and scalable, suitable for businesses of all sizes, especially those looking for a versatile tool that can manage both workforce operations and IT needs.

Rippling also provides strong compliance features, automating tax filings and ensuring businesses stay up to date with federal and state regulations.

Features & Benefits:

• Payroll Management: Automates payroll processing, tax filings, and compliance across all 50 U.S. states and internationally.
• HR Management: Manages employee data, onboarding, offboarding, benefits, and performance tracking within a single platform.
• IT Management: Automates the setup and management of employee devices, software, and apps like Slack, Google Workspace, and Office 365.
• Benefits Administration: Streamlines employee benefits management, including health insurance, 401(k) plans, and workers’ compensation.
• Time and Attendance: Tracks employee work hours, integrates with payroll, and manages paid time off (PTO) and scheduling.
• App and Device Management: Sets up and manages employee access to company tools and applications, including onboarding/offboarding workflows.

Pricing: For pricing, you need to request a quote.

Account: It doesn’t allow you to create an account. You can schedule a 30-minute demo.

Conclusion

Choosing the right Payroll that integrates with QuickBooks is crucial for efficient business operations. Integrating payroll solutions like Gusto, QuickBooks Payroll, Paychex Flex, ADP Workforce Now, or Rippling with QuickBooks Online enhances efficiency by automating workflows, ensuring compliance, and providing advanced reporting capabilities.

Custom QuickBooks integration services can address specific business needs, offering tailored solutions for seamless operations. Whether you’re a small business owner or managing a large enterprise, these integrations can transform your payroll management process, saving time and reducing errors.

Discover the best fit for your business and unlock new levels of productivity with integrated payroll that integrates with QuickBooks.