🔗 Integrating with QuickBooks

Easily connect your payroll data to your accounting system with a few clicks.

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Overview

Whether you're a small startup managing five employees or an enterprise scaling toward 200+, FlexPay ensures that payroll and accounting don’t operate in silos. They speak the same language, they reconcile in real-time, and they leave a transparent trail of documentation. You no longer need to rely on Slack messages to your accountant or late-night emails asking if payroll was properly categorized. With this integration, your general ledger becomes an extension of your payroll system. And once it’s set up, it just works.

The QuickBooks Integration feature of FlexPay provides seamless compatibility with both QuickBooks Online and QuickBooks Desktop environments. It’s built to reflect the reality of most companies: some have already embraced the cloud, while others remain on traditional local installs. Regardless of where you fall, FlexPay has you covered.

This section builds on critical setup steps you’ve already completed—like 🏦 Bank Setup, 👔 Role Configuration, and 🧾 State Tax Filings. Each of those directly affects how data flows to your books. For example, accurate direct deposit rules and deduction structures directly impact which QuickBooks accounts your journal entries will use.

🟩 Glossary Highlight: 🟩 General Ledger Mapping is the process of assigning specific FlexPay categories (e.g., gross pay, benefits, tax liabilities) to matching accounts in your accounting software.

The integration allows you to:

• Sync gross pay, taxes, deductions, and net pay to specific ledger accounts.

• Automatically generate payroll journal entries.

• Reduce manual reconciliation and risk of error.

• Ensure your books match your payroll data—down to the penny.

Let’s dive into both methods of integration.

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🔁 QuickBooks Online Integration

Step-by-Step Walkthrough

Figure 1. Interface to Create a Direct Deposit in FlexPay

Connecting to QuickBooks Online is done directly through FlexPay’s Integrations settings:

1. Navigate to Settings → Integrations → QuickBooks Online.

2. Click the Connect to QuickBooks button.

3. You’ll be redirected to a secure OAuth window where you’ll log in with your Intuit credentials.

4. After approval, you’ll be asked to map your FlexPay fields to ledger accounts in QuickBooks.

⚠️ Reminder: You must be both a FlexPay Admin and a QuickBooks Admin to complete this step. A mismatch in permissions will result in authentication failure.

Once authenticated, you’ll be guided through an interactive ledger mapping wizard.

🧾 Mapping Table

Payroll Field	Suggested QuickBooks Account
🟩 Gross Wages	Wages Expense
🟩 Federal Taxes Withheld	Tax Liabilities
🟩 Benefit Deductions	Pre-Tax Benefits Payable
🟩 Employer Contributions	Employer Liabilities
🟩 Net Pay	Payroll Clearing Account

🧠 Why map? This allows FlexPay to automatically generate balanced journal entries per payroll cycle. These appear in QuickBooks as draft entries (Online) or synced entries (Desktop), ready for review or posting.

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🖥️ QuickBooks Desktop Integration

Local Sync Tool

Figure 2. Integration Setup Screen Showing Quickbooks Connection and Sync Now and Sync Settings

For customers using QuickBooks Desktop, FlexPay offers a small Windows utility that allows secure two-way communication between your payroll data and local company file:

1. Download the sync tool from Settings → Integrations → QB Desktop.

2. Install on the same PC as your .QBW QuickBooks file.

3. Open QuickBooks and ensure it’s in multi-user mode.

4. Launch the FlexPay Sync app and follow the configuration wizard.

The wizard will:

• Ask for your FlexPay API token.

• Connect to your local QuickBooks company file.

• Prompt you to map payroll fields to chart-of-account entries.

• Schedule automated sync frequency (e.g., hourly, daily).

🟨 Hint: Desktop users must keep QuickBooks open during sync unless background sync permissions are granted via Intuit’s SDK prompt.

Table: Desktop Sync Settings

Setting	Example Value
Sync Frequency	Daily @ 5:30 PM
Connection Type	Localhost to FlexPay API
Employee Mapping	Auto-detected by name/email
Chart of Accounts	Pulled live from QB Desktop

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🔍 Confirming Sync & Auditing

After setup, FlexPay will automatically post each payroll as a journal entry in QuickBooks. You can verify sync status from:

• Reports → Journal Sync Logs

• Integrations → QuickBooks → Last Sync Details

Each log includes:

• Payroll ID

• Posting status

• Timestamp

• Mapped ledger accounts

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✅ Summary

Once you’ve integrated QuickBooks with FlexPay, your entire payroll operation becomes book-accurate in real-time. There’s no more copy-pasting from spreadsheets, no more guesswork about tax liabilities, and no delay in reconciling pay runs. As long as you’ve configured your 🟩 benefits, 🟩 roles, and 🟩 state tax settings properly, the integration will reflect those settings automatically in each ledger transaction.

For finance teams, this integration is a game-changer—it means less work, better data, and fewer audit headaches. It also allows for stronger collaboration between your HR/payroll team and accounting department.

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🚀 What’s Next?

👷 Paying Contractors Only – Handle 1099 contractors with the same power and simplicity as W-2s.

If you’ve ever struggled with managing freelancer invoices, off-cycle payments, or 1099 year-end reporting, FlexPay has a dedicated workflow built just for you. In the next section, we’ll explore how to create contractor-only pay runs, link contractor payments to your general ledger, and auto-generate 1099s when tax season arrives.