QuickBooks Online Paylocity Integration: How to Connect with the QuickBooks


Last Update: July 4th, 2025     Author: Adams Williams

Reviewed By: SMBAccountants Editorial Team

Most business personnel will attest to how managing payroll and accounting becomes more complicated as the business scales new heights. To make these tasks easier, most firms rely on application tools, and some of them include Paylocity and QuickBooks. Both on their own, the tools can reduce the number of processes necessary, but when used together, their integration can be ten times more effective. In this article, we explore the pros, how-to, and checklist for using Paylocity with QuickBooks to meet your needs more effectively.

Table of Contents

Understanding Paylocity and QuickBooks

Paylocity is a cloud-based payroll and human capital management application that was developed to simplify tax compliance and payroll processing as well as the performance of other duties by the HR. Some of the tools provided include time tracking and benefits administration, together with portals for self-service by the employees.

QuickBooks is the accounting software that was invented by Intuit, with money management and expense tracking, plus automatically generating reports related to the company’s finances. QuickBooks is very useful among SMEs mainly because it holds strong capability together with ease-of-use in their interface.

Steps for QuickBooks Online Paylocity Integration

QuickBooks integration makes Paylocity easy to use when it comes to transferring data between the two in terms of payroll and financial data, to eliminate instances of the entry of wrong data by its users. See steps below:

Step 1: Verify System Requirements

  • Ensure that you have the administrative privilege to both Paylocity and QuickBooks.
  • Confirm compatibility:
    • Paylocity is generally integrated with either QuickBooks Desktop or QuickBooks Online.
    • Look for other integration tools or software such as Paylocity Data Connector.

Step 2: Set Up Paylocity for Integration

  • Log in to Paylocity:
    • Go to the administrator portal.
    • Go to File Feeds or Integrations settings.
  • Turn on Export Settings:
    • Configure payroll export options to work with QuickBooks.
    • Export file format, say IIF for QuickBooks Desktop or CSV for QuickBooks Online.

Step 3: Payroll Data Mapping

  • Associate Paylocity categories with QuickBooks account codes of wages, taxes, deductions, and benefits.

Step 4: Set up QuickBooks to Import the Payroll

  • For QuickBooks Desktop:
    • If not installed, download the IIF import tool.
    • Make your Chart of Accounts align with your payroll categories within Paylocity.
    • Set up vendor accounts for payroll taxes, benefits, or garnishments.
  • QuickBooks Online:
    • Ensure the CSV import is turned on
    • Payroll category must match how Paylocity is set to export.

Step 5: Set up Integration

  • Direct Export/Import:
    • Export your payroll data from Paylocity in whatever format is accepted by QuickBooks.
    • Import the file into QuickBooks using a feature called IIF Import for Desktop or CSV Import for Online
  • Optional Automated Connectivity:
    • Third-party connectors can be Zapier or a custom API
    • To connect Paylocity with QuickBooks, follow any linking instructions.
    • Run the automated data transfer flow test.

Step 6: Map Data Fields

  • Map fields in QuickBooks to corresponding fields in Paylocity:
    • Wages → Payroll Expenses
    • Taxes → Payroll Tax Payable
    • Eliminations → accounts payable
  • It has only one function called Save Mapping Settings, which saves the mapping field settings instead of new settings for re-import with the same data.

Step 7: Test the Integration

  • Do a test payroll export and import.
  • Reconcile data in QuickBooks:
    • Verify that totals for wages, taxes, and deductions match Paylocity reports.
    • Check account classifications.
  • Address discrepancies by adjusting the mapping or settings.

Step 8: Schedule Regular Updates

  • Determine the frequency at which payroll data is exported and imported (for example, weekly or per pay).
  • Automate or develop a routine for this process to ensure up-to-date financial records.

Step 9: Train Staff and Monitor

  • Train relevant staff on the integration workflow.
  • Regularly review and audit the data for any inconsistencies.

You may read this: AppFolio QuickBooks Integration

Paylocity vs QuickBooks Desktop

Two different products, Paylocity and QuickBooks Desktop, are designed to address different aspects of your business. You can determine which one will be most suitable for your situation by comparing the two to see which has the strongest points:

Benefits

  • Payroll management: With automated tax computations, filings, and compliance, payroll processing has been reduced.
  • HR applications: Provide time tracking, benefits administration, performance reviews, and employee engagement.
  • Cloud: Accessible online from anywhere in the world; updates occur automatically.
  • Employee Self-Service: Employees may examine their pay stubs, request time off, change personal information, and more through employee self-service.
  • Integration: Additionally, it interfaces with other technologies, including benefit providers, ERP systems, and accounting applications.

Suitable for

  • Medium- to large-sized companies in need of more reliable HR and payroll systems.
  • Businesses that use a distributed workforce need access to the cloud.
  • Organizations that prioritize enhancing their HR processes and employee engagement.

Potential Negative Effects

• More expensive than simpler payroll solutions.

• Far less feature-rich than more comprehensive invoicing or accounting.

Strengths

  • Accounting Capability: Bookkeeping, invoicing, expense tracking, and financial reporting capabilities are included.
  • Payroll Add-On: It has payroll features available as an optional service for additional fees.
  • Customization: You can deeply customize invoices, reports, and other settings.
  • Offline Access: Desktop-based allows access even without an Internet connection.
  • Industry-Specific Versions: Offers tailored features for different industries (e.g., contractors, non-profits, manufacturing).

Best Suited For

  • Small to medium-sized businesses that mainly operate in accounting and bookkeeping.
  • Companies that do not need heavy HR functionalities.
  • Users who want data storage on their computer rather than a cloud-based environment.

Potential Weaknesses

  • Only manually update if you are on an annual subscription.
  • Fewer collaborative capabilities compared to a cloud-based product.
  • Payroll functionalities are not as robust as Paylocity, which is an application-specific HR.
Paylocity vs QuickBooks Online

You may read this: Zoho QuickBooks Integration

Benefits and Features of Paylocity QuickBooks Online Integration

Businesses wishing to simplify their accounting and payroll procedures can gain many advantages by integrating Paylocity with QuickBooks. Below are the main benefits:

1: Efficiency and Automated Systems

  • Payroll information should automatically post to QuickBooks, saving the effort in data entry.
  • Minimize human mistakes in manual data entry to guarantee more accurate financial records.

2: Time Conserving

  • This QuickBooks automation package automates such repetitive processes as importing employee payments, payroll costs, and tax withholdings.
  • This enables the accounting and HR departments to spend more time on strategic tasks.

3: More Accurate

  • This will ensure that payroll information, such as wages, taxes, and deductions, is mapped to the proper QuickBooks accounts.
  • That ensures there is a lower possibility of disparity in payroll account and financial book balances.

4: Time data synchronization

  • It makes real-time payroll data accessible to businesses to check the real-time health of their financial system.
  • QuickBooks also ensures on-time filing and adherence to the tax laws.

5: Reporting and analysis improved

  • All comprehensive reports from accounting and payroll are made through a combination.
  • This enables one to analyze labor costs, profitability, and other financial variables more effectively.

6: Easier Tax Compliance

  • QuickBooks also saves on time preparing and filing taxes since the taxes withheld and payments made are automatically recorded.
  • It reduces the possibility of errors, which may attract fines or audits.

7: Scalability

  • Gets organizations to grow through automation of accounting and payroll functions, easier to manage a growing workforce and financial complexity.

8: Saving money on the expense

  • It helps reduce the burden of administrative paperwork that may, in turn, provide cheaper labour.
  • Incorrect entries can be avoided from fines or costly repairs.

9: Easy Integration

  • Integration is easy to do even by non-technical people due to the setup options and intuitive tools.
  • Due to synchronization options, businesses may personalize the connection according to their specific needs.

10: Data Security

  • Ensures safe transfer of data between Paylocity and QuickBooks while protecting sensitive employee and financial information.
  • Both sites meet the standards for data protection.

11: Streamlined Employee Management

  • It centralizes employee data, including salaries, benefits, and tax information, for easier management and tracking.
  • It simplifies onboarding and payroll changes.

Several features of the Paylocity QuickBooks Integration help organizations automate payroll and several financial activities. The salient characteristics of this integration are as follows:

1: Syncing Data Automatically

  • Sync payroll information from Paylocity to QuickBooks automatically, including wages, taxes, and deductions.
  • Automatically updates financial data without the need for human involvement.

2: Personalized Account Mapping

  • Enables companies to link payroll information to certain QuickBooks accounts.
  • Allows for customized setups to match particular chart-of-accounts designs.

3: Current Information

  • This maintains the integrity of the QuickBooks account and allows for close-to-real-time payroll information transfer.
  • This helps companies in tracking their cash flow and expenses with high accuracy.

4: Payroll Expenses Grouping

  • Payroll expenditures automatically classify and could comprise taxes, benefits, and compensation to the employees.
  • A detailed analysis divides prices by region, job function, or department.

5: Employee Record Sync

  • Synchronizes employee data, such as name, pay rate, and deductions, between the two systems.
  • Streamlines employee management with onboarding and offboarding.

6: Tax Data Sync

  • Syncs tax withholdings, employer contributions, and filings directly with QuickBooks.
  • Accurate and compliant reporting is made easy.

7: Flexible Integration Options

  • Fully supports both online and desktop QuickBooks.
  • Flexibility to accommodate business users of different QuickBooks versions.

8: Error Notifications and Logs

  • It gives error messages for failed data transfer or mismatch, which are corrected quickly.
  • The import log for data will be kept as it aids auditing and troubleshooting processes.

9: Customized Reporting

  • Allows personalized financial reporting for summarizing accounting and payroll data.
  • Supports the tracking of tax liability, labor costs, and other financial performance measurements.

10: Secure Data Transfer

  • It utilizes encryption and other types of security measures to ensure sensitive payroll and financial data remain safe during the syncing process.
  • It ensures the fulfillment of data protection standards by industries.

11: Scheduled Imports

  • Payroll data can be configured to import periodically, say, weekly or biweekly transfers.
  • It reduces the manual effort and ensures data updation consistently.

12: Multi-Company Support

  • Multi-Company Support handles payroll and accounting for several companies or subsidiaries under one QuickBooks account.
  • This simplifies procedures for organizations having complex design layouts.

14: Audit Trail and Compliance Support

  • It has an audit tracking and support by recording all the modifications made along with the changes between QuickBooks and Paylocity in case of an audit.
  • It ensures that financial and payroll information is compliant with legal and regulatory requirements.

15: User-Friendly Interface

  • It offers an easy setup for non-technical users.
  • Provides intuitive dashboards and settings for managing integration preferences.

16: Scalable Design

  • Adapt to growing businesses and to their needs to keep pace with volumes of payroll and financial data.
  • Suitable for small businesses and enterprises alike.

Also read this: Toggl Integration with QuickBooks

Conclusion

Integrating Paylocity with QuickBooks is a strategic action for a business that intends to improve its payroll and accounting operations. The entire integration process enables the automatic transfer of data, enhances accuracy, and simplifies compliance, thus providing a basis for effective decision-making. Whether using manual methods or third-party tools, following best practices and proactively addressing identified challenges will guarantee success in integrating processes.

Investing both your time and resources in this integration will surely change the financial health and operational efficiency of your business, and is therefore a valuable investment for businesses both small and large. Don’t hesitate to reach out to Paylocity support or QuickBooks when you’re having issues, or hire an integration expert to assist you.

Frequently Asked Questions

Q 1: What are the common mistakes in integration, and how to fix they?

Q 2: Can I customize how payroll data maps into QuickBooks?

Q 3: Are there any fees associated with the integration?

Q 4: How often should I sync Paylocity with QuickBooks?

Q 5: What data is transferred in the course of integration?

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