This guide walks you through:

• Installing PayTraQer from QuickBooks Online

• Connecting your BigCommerce store

• Setting the key sync options so your BigCommerce sales, fees, and payouts land in the right accounts in QuickBooks Online

The article is written for users who are new to PayTraQer and want a clean, reconciliation-ready setup.

Prerequisites

Before you start, make sure you have:

• An active QuickBooks Online company

• Company admin access in QuickBooks Online

• An active BigCommerce store with login credentials

• PayTraQer available from the QuickBooks App Store in your region

Step 1: Install PayTraQer from QuickBooks Online

1. Sign in to QuickBooks Online as a primary admin.

2. Go to Apps in the left menu.

3. Search for PayTraQer.

4. Click Get app now.

5. Choose the QuickBooks Online company you want to connect, then click Connect.

6. Grant access when QuickBooks prompts for permission.

After the connection is successful, PayTraQer opens in a new tab and starts your 15-day free trial.

Pick your Sync Mode

Right after connecting to QuickBooks, choose how BigCommerce data should post.

• Consolidated Sync (Sales Summary): fewer entries and faster reconciliation

• Itemized Sync (Individual): customer and item detail in QuickBooks

Select one and click Get Started. You can change this later in settings.

Step 2: Connect your BigCommerce store to PayTraQer

Once your QuickBooks company is linked, connect BigCommerce.

First-time connection

1. In PayTraQer, you will be prompted to connect a payment gateway or e-commerce channel.

2. Click Add E-commerce Accounts.

3. On the Connect to E-commerce screen, choose the BigCommerce tile.

   

4. Log in to BigCommerce when prompted.

   

5. Select the BigCommerce store you want to connect.

6. Grant permissions for PayTraQer to read orders, refunds, and related data.

You will see a success message when BigCommerce is connected.

If you skipped this during onboarding

1. In PayTraQer, go to Connectors in the left menu.

2. Open E-commerce Accounts.

3. Click Connect next to BigCommerce, then follow the same login and approval steps.

Step 3: Express Settings for BigCommerce

After you connect BigCommerce, PayTraQer shows a simple Express Settings screen. This sets your default accounts so that transactions from BigCommerce land in the right place in QuickBooks Online.

On the Express Settings panel:

• Your sales will be recorded in

  • Choose your BigCommerce Bank Account.

  • This is a clearing account that temporarily holds BigCommerce sales and fees until payouts reach your real bank account.

  • Best practice: use a dedicated clearing account such as “BigCommerce Bank Account” instead of your main checking account.

• Fees will be recorded in

  • Select the BigCommerce Fees expense account (or another fee expense account you prefer).

  • All BigCommerce payment fees will post here.

• Do you want to process the payouts / settlements

  • Turn this On if you want PayTraQer to create Transfer transactions from the BigCommerce clearing account to your real checking account.

  • Keep it Off if you prefer to handle deposits manually.

Click Save Setting when you are done.
You can change these later from the Sync Settings / BigCommerce screen.

• Auto download
  After saving, PayTraQer automatically downloads the last 60 days of BigCommerce data.

• More history
  Use Download historical transactions to pull other date ranges with From and To filters.

• Auto Sync
  Turn on Auto Sync to download and post new transactions.

Step 4: Review Sync Settings for BigCommerce

To fine-tune how BigCommerce data posts to QuickBooks Online:

1. In PayTraQer, go to Customizations or Settings (depending on your layout).

2. Open Sync Settings.

3. Choose BigCommerce from the connector dropdown.

You will see tabs for Sales, Product & Services, Tax, Fees, Payout, and Payment Processors.

4.1 Sales settings

This tab controls where BigCommerce sales and customers are recorded.

Accounts

• Bank Account to deposit your sales/income

  • Recommendation: keep this set to your BigCommerce clearing account so sales, fees, and payouts all flow through the same account.

• Payment methods to track your transactions

  • This label will appear in QuickBooks as the Payment method on sales.

• Do you want to configure separate GL accounts for your payment system

  • Turn this on only if you need different income or clearing accounts for different processors linked to BigCommerce.

• Record the Sales as

  • Options typically include Sales Receipt or Invoice.

  • For most BigCommerce stores (paid at checkout), use Sales Receipt.

  • Use Invoice only if you invoice first and collect the payment later.

Customers

• Do you want to create Customer automatically if it does not exist in your QuickBooks
  

  • PayTraQer creates customers when it does not find a match in QuickBooks.

• Common Customer for your Sales Transactions
  

  • Keep this Off if you want individual customers for each order.

  • Turn it On and select a generic customer (for example, “BigCommerce Online Customer”) if you want to avoid thousands of individual customer records.

• Customize Customer Matching

  • Use this to control how PayTraQer matches buyers from BigCommerce to existing customers in QuickBooks.

Tracking

• Location / Department for your Sales transactions

• Class for your Sales transactions

Set these if you use Location or Class tracking in QuickBooks Online. Every synced sale from BigCommerce will carry these values.

Sync

• Do you want to skip the sales & process the associated fees only
  

  • Use Yes only if your sales are already recorded by another system and you want PayTraQer to bring in just the BigCommerce payment fees.

4.2 Product & Services settings

This tab controls how items from BigCommerce map to QuickBooks Products and Services.

Auto Creation

• Do you want to create Products/Services automatically

  • Turn this off if you do not want new items created in QuickBooks.

• Select Products/Services Type to create items automatically when it does not exist

  • Choose the default item type, such as Non-inventory or Service, for any new products PayTraQer creates.

• Select Income Account for the Products/Services associated with your transactions
  
  

  • Choose the income account for item-level sales (for example, Sales of Product Income).

Match Product

• Match Product by

  • Options usually include Name or SKU.

  • Pick the one that matches how you manage items between BigCommerce and QuickBooks.

• Customize Product Matching

  • Add rules if product names or SKUs differ between systems.

Common Item

• Do you want to use common product/service for all your sales

  • Keep this Off if you want item-level detail in QuickBooks.

  • Turn this On if you prefer to post all BigCommerce sales to a single item (for example, “BigCommerce Sales”).

• Select common product/service

  • Choose the item to use when the common item option is enabled.

4.3 Tax settings

Use this tab to control how BigCommerce sales tax posts in QuickBooks Online.

• Do you want to calculate and apply tax automatically for all your sales & expenses

  • PayTraQer calculates tax amounts based on data from BigCommerce and applies them to synced transactions.

• Tax Included in Payments

  • Enter the tax Percentage(%) for direct payments received

  • Enter the tax Percentage(%) for Shipping

  • Use these fields if your payments or shipping charges are tax-inclusive.

• Tax Code

  • Select a common Tax Code to apply across all transactions when needed.

  • After your first sync, open a sample sale in QuickBooks and confirm that tax amount and code look correct.

4.4 Fees settings

This tab controls how BigCommerce fees are recorded.

Fees

• Select Vendor who receives the Payment Fees

  • Example: Bigcommerce.

  • This becomes the vendor on fee expenses in QuickBooks.

• Select Fee Category to record the expenses

  • Example: Bigcommerce Fees.

  • Choose the expense account for payment fees.

• Bank Account to record Payment Fees

  • Example: Bigcommerce Bank Account.

  • Best practice is to use the same clearing account as your sales so that fees and sales settle together.

• Do you want to configure separate GL accounts for your payment system

  • Turn this on only if you need different fee accounts per processor.

Auto Tax Calculation for Fees

• Class for your Fees

• Location/Department for your Fees

Set these if you track class or location on expenses.

• Do you want to skip the fee details from syncing

  • Keep this off so that fees post as separate expense lines and your net payouts reconcile cleanly.

4.5 Payout settings

Payout settings control how PayTraQer handles BigCommerce payouts or settlements into your real bank account.

• Do you want to process the payouts / settlements

  • Turn this On to create Bank Transfer transactions from the BigCommerce clearing account to your Checking account.

When this is enabled:

• BigCommerce sales and fees stay in the clearing account.

• Payouts move the net amount to your real bank account.

• Your clearing account should trend toward zero after each payout cycle, making reconciliation easier.

Use the link on this screen to review the difference between a Clearing Account and a Checking Account if needed.