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Square QuickBooks Integration – Complete Guide

Connecting your payment platforms to your bookkeeping software is a masterstroke to elevate your business to new luring heights. Learn more about square QuickBooks Integration here.

Talking about QuickBooks Square Integration, you can attain complete flexibility and achieve neat and accurate automated results in terms of cash flow, profit margins, and more.

This article covers in detail Square QuickBooks integration, you can find answers to all your doubts regarding the Square Quickbooks sync in this read.

Before diving into how to use PayTraQer for Quickbooks and Square, let’s zoom into how PayTraQer connects Square and QBO.

PayTraQer helps you connect with your payment gateways, in this case, we will be using Square to synchronize all your online payments including payment fees and expenses. The powerful rollback feature enables complete data control over your bookkeeping.

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How to Connect Square with QuickBooks?

To begin with, you are required to connect your Quickbooks company with PayTraQer.

Connecting QuickBooks Online with PayTraQer takes you only minutes and the procedure is simple. We have listed the step-by-step procedure to connect PayTraQer and QuickBooks.

You Can Follow Any of the Two Methods:

  1. Intuit App Store
  2. QuickBooks Apps Menu

From Intuit App Store:

  • From the Intuit app store, click ‘Get App’ button, and search for “paytraqer” in the search bar.
  • Authorize “PayTraQer” to connect with your QuickBooks Account.

From QuickBooks App Menu:

  • Log in to your Quickbooks account.
  • From the ‘Apps’ menu, click on ‘find apps’ tab.
  • Search for ‘paytraqer’ in the search bar provided.
  • Click on ‘Get App Now’.
  • Select the PayTraQer app and authorize “PayTraQer” to connect with your QuickBooks Account.

After connecting your Quickbooks account, you will be navigated to the payment systems menu screen. Select Square and click the connect button. You will be redirected to the Square application screen for granting permission.

Please note that you can disconnect at any time from the settings. Next, click on the Allow button to authorize the connection. You will be redirected back to the PayTraQer screen.

Sync Square Transactions to Quickbooks Online

Once the connection is successful, PayTraQer will automatically record your Square transactions.

There are two methods to sync your Square Transactions in QuickBooks,

  • Auto-sync
  • Manual-sync


With the Auto Sync feature, you can automate your current ongoing Square transactions with QuickBooks without any manual entries. This ensures accurate Square transaction reports at any time. To enable the feature, Check the ‘Sync Automatically’ button.


The Manual sync option requires manual intervention to record both the historic and current Square transactions on the PayTraQer dashboard. The good part about manual syncing is that you get complete control over the transactions that are required to sync.

You can easily ignore the transactions that are not required to be synced. After syncing, the transactions are available in the synced/error tab with detailed transaction information on the transaction dashboard.

If you find any changes with the reports post sync, you can always roll back or withdraw your synced transactions to the previous state.

Record Historic Square Payments in QuickBooks Online

Once you have completed configuring the settings, QuickBooks will automatically transfer the previous transactions from your Square account.

And in case you want to record historic Square Transactions before 30 days, If you’re using online banking to download some of these transactions, you need to be aware that it can record up to 90 days of downloads from Square. By the way, you can import previous historical transactions to QuickBooks Online from Square.

Square QuickBooks Integration with PayTraQer

Next, we will have to configure some simple settings to accurately configure your Square account preferences. Check the below-mentioned settings at your convenience to complete the configuration process.

  1. Sales Preferences: This setting will govern how your Square sales transactions will be recorded in your QuickBooks. The default values provided will be automatically created in QuickBooks and are recommended for accurate bookkeeping.
  2. Product Settings: This configuration will determine how the Products/Services are synced. If the feature “Create Product/Services automatically” is turned ON, then missing items in your QuickBooks will be auto-created during the sync.
  3. Tax Settings: Enabling this setting will sync with tax calculation. Otherwise, the tax amount will be added to the transaction amount and recorded without tax.
  4. Fee Settings: This setting will govern how the Square fee details get recorded in your QuickBooks. You can add the default vendor, expense category, and expense bank account for creating the expense transaction corresponding to the Square fees component.
  5. Expense Settings: Set the default vendor, expense category, and expense bank account for creating the expense transactions corresponding to the Square transactions.
  6. Payout Settings: Enable the “Process the Payout” option with the “Transfer To” account, so that all your Square Payouts get processed as Transfer transactions in your QuickBooks and will be very handy during reconciliation.

Your Square payments are all set for the syncing process with your Quickbooks.

Benefits of Square QuickBooks Integration

Square integration with Quickbooks Online will have multiple benefits for small business owners. Some of the features include:

  • You can automatically import Square invoices, Square Payments, and Square deposits into your Quickbooks account easily. You do not need to manually import the payments.
  • If the product name already exists in your Quickbooks, you can easily preserve all the data related to the product including discounts, taxes, tips, and sales data.
  • You can also import Square refunds into your Quickbooks.
  • You can enter the credit card payments in batches as deposits and thus, be easily reconciled.


Therefore let’s cut to the chase and give you our verdict on integrating Square and Quickbooks. Save time and venture into new forms of business flexibly by integrating your Quickbooks Online account with Square using PayTraQer.

Discover new paths as your business accounts will be always backed with Quickbooks. We hope this article helped you learn the basics, procedures, and benefits of Quickbooks Square Integration.

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