How to Connect Amazon with QuickBooks Online using PayTraQer

Use PayTraQer to bring your Amazon settlements, sales, fees, and tax entries into QuickBooks Online in a clean, automated way.

This guide walks you through:

• Connecting Amazon and QuickBooks Online to PayTraQer

• Doing a quick setup with Express Settings

• Fine tuning Sales, Product, Tax, Fees, and Payout mappings

• Downloading and syncing your Amazon transactions

Prerequisites

Before you start:

• A QuickBooks Online company connected to PayTraQer

• Access to your Amazon account used for payouts

• Admin rights in QuickBooks to create accounts, items, and classes if needed

Connect QuickBooks Online to PayTraQer

If your QuickBooks company is not already connected:

1. Sign in to PayTraQer.

2. Choose Connect to QuickBooks and follow the prompts.

3. Allow PayTraQer to access your QuickBooks company.

Once connected, you will see your QuickBooks company name at the top of PayTraQer.

Choose Your Sync Mode

After connecting to QuickBooks, decide how Amazon data should post:

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

• Itemized Sync (Individual): detailed entries with customer and item information.

Select your preferred mode and click Get Started.

Add your Amazon account in PayTraqer

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

2. Open the Ecommerce Connectors tab.

3. Click Add New, choose the Amazon card.

Sign in to your Amazon account when prompted and approve access.

After a successful connection, you will see Amazon Account listed under Ecommerce Connectors.

Configure Express Settings for Amazon

Right after connecting, PayTraQer shows the Express Settings screen for Amazon. This is a quick way to get started with the most common settings.

Here you can choose:

• Amazon Bank Account

  • The bank or clearing account where your Amazon sales and payouts will be recorded.

• Fees will be recorded in

  • The expense account to store Amazon fees, such as Amazon Advertisement Fees.

• Sales Tax will be recorded in

  • The account used for Amazon tax components, such as your Amazon Reserve Account.

• Do you want to process the payouts / settlements?

  • Turn this on if you want PayTraQer to create transfer entries that move funds from your Amazon clearing account to your actual checking account.

  • Once enabled, choose the Settlement Bank Account where payouts land in QuickBooks.

Click Save Setting when you are done.
You can change these later from Settings → Amazon → Payout and Fees.

Download Amazon Transactions

Once your settings are in place, you can bring in your Amazon data.

Download recent and historical data

• After connecting, PayTraQer automatically starts downloading your 60 days Amazon transactions.

• To pull older data, use Download Historical Transactions in the Transactions screen.

Auto Sync

• When enabled, PayTraQer regularly downloads and syncs new Amazon transactions with QuickBooks.

You will see all imported records under Transactions → Review.

Fine Tune Amazon Sync Settings

To access detailed controls:

1. Go to Settings in the left menu.

2. Choose Amazon from the connector list.

3. Use the tabs: Sales, Product & Services, Tax, Fees, Payout, Payment Processors.

5.1 Sales Settings

Accounts

• Bank Account to deposit your sales/income

  • Set this to your Amazon clearing or bank account where all sales entries will post.

• Payment methods to track your transactions

  • Choose Amazon so that all Amazon sales use a consistent payment method in QuickBooks.

• Record the Sales as

  • Choose whether PayTraQer posts Amazon sales as Invoice or Sales Receipt based on your workflow.

Customers

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

  • Turn this on to let PayTraQer create new customers when a match is not found.

• Common Customer for your Sales Transactions

  • Use this if you prefer to record all Amazon sales under a single customer (for example “Amazon Marketplace Customer”) instead of separate names for each buyer.

• Customize Customer Matching

  • Add rules to map Amazon buyer names to your preferred customer names in QuickBooks.

Tracking

• Location/Department for your Sales transactions

  • Set a fixed location or department for Amazon sales.

• Class for your Sales transactions

  • Assign a class for easier reporting of Amazon activity.

Sync

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

  • Turn this on if you only want to sync Amazon fees into QuickBooks and not the sales details.

Product and Service Settings

Auto Creation

• Do you want to create Products/Services automatically?

  • Enable this so PayTraQer can create items when an exact name match does not exist.

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

  • Choose Non Inventory or Service based on how you track your Amazon items.

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

  • Choose the income account for auto created items, such as Sales of Product Income.

Match Product

• Match Product by

  • Choose Name (or SKU if available in future) for item matching between Amazon and QuickBooks.

• Customize Product Matching

  • Add mapping rules if your Amazon item names differ from QuickBooks item names.

Common Item

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

  • Enable this if you want to post all Amazon sales to a single default product or service in QuickBooks.

• Select common product/service

  • Pick the item to use as this default.

Tax Settings

Auto Tax calculation

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

  • Turn this on to let PayTraQer handle tax for Amazon sales and related expenses.

Tax Accounts Mapping

Map different tax components that appear in Amazon settlements:

• Sales Tax

• Shipping Tax

• Giftwrapping Tax

• Withheld Tax

For each, choose the correct account in QuickBooks (for example an Amazon reserve or tax liability account). This keeps your tax reporting accurate.

Fees Settings

Fees

• Select Vendor who receives the Payment Fees

  • Set this to Amazon so all fees are tied to the Amazon vendor.

• Select Fee Category to record the expenses

  • Choose the expense account such as Amazon Advertisement Fees or a general Amazon Fees account.

• Bank Account to record Payment Fees

  • Select the bank or clearing account used to hold fee entries.

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

  • Turn this on if you want detailed accounts per fee type.

Auto Tax Calculation

• Class for your Fees

  • Assign a class for all Amazon fee expenses.

• Location/Department for your Fees

  • Assign a location or department for fee entries.

• Do you want to skip the fee details from syncing?

  • Enable this if you only want summary level data and do not need each fee broken out.

Fees Category Mapping

For detailed mapping, you can assign different accounts for specific Amazon fee types such as:

• Commission Fee

• Fixed Closing Fee

• Referral Fee

• Variable Closing Fee

• Subscription

Choose the right expense account for each category.

Payout Settings

Control how Amazon payouts and reserve balances are recorded.

• Do you want to process the payouts / settlements?

  • Enable to sync each settlement as a transfer from your Amazon clearing account to your settlement bank account in QuickBooks.

• Do you want to track amazon current reserve balance

  • Turn this on to track the running reserve balance Amazon holds.

• Transfer the current reserve balance to this account

  • Choose the account where reserve transfers should be posted when Amazon releases funds.

Review and sync

1. Go to Transactions → Review.

2. Use the filter to view specific transaction types such as Invoice Payment, Expense, or Customer Refund.

3. Select one or more transactions.

4. Click Sync.

A pop up confirms what was created, for example:

• Payment

• Invoice

• Fees

with successful and failed counts.

Check synced results

1. Open the Synced tab to see all synced Amazon transactions.

2. Use the Details button to open the right side panel.

3. In the Synchronization Details panel you can see:

   • Invoice created

   • Payment created

   • Individual fee entries created

   • Links to Open in QuickBooks for each transaction

If you need to roll back a sync, use the Undo button on the Synced list to delete the related QuickBooks entries that PayTraQer created.

Track sync history

The Sync History tab shows daily totals:

• Number of transactions synced

• Total sales, fees, and other components

• Any failed sync counts

Use this to confirm everything from Amazon is flowing into QuickBooks as expected.

Best Practices

• Keep QuickBooks banking rules disabled for the same Amazon bank account to avoid duplicate entries.

• Review Express Settings first, then adjust detailed mappings once you see a few synced settlements.

• Use Sync History regularly to spot any mapping issues early.