Amazon Pay vs. Amazon Seller Central: A Critical Distinction

Before opening a single report, every bookkeeper must understand the difference between Amazon Pay and Amazon Seller Central — they are completely separate platforms with different reconciliation workflows, different reports, and different QBO setups.

Amazon Seller Central is for merchants selling products on Amazon.com as a marketplace. It produces bi-weekly settlement reports bundling FBA fees, referral fees, storage fees, advertising, and refunds. Most "Amazon + QuickBooks" guides on YouTube refer to this.

Amazon Pay is a payment gateway that lets customers check out on your own website (Shopify, WooCommerce, BigCommerce, custom-built stores, etc.) using their Amazon account credentials and payment methods. It is the equivalent of Stripe or PayPal — but the buyer experience is powered by Amazon's login and stored payment info. The seller receives payouts from Amazon Payments, Inc., not from Amazon.com Seller Central.

If your client says "we use Amazon Pay," they mean customers are checking out on their own website using Amazon Pay as the payment button — not that they sell on Amazon. The two platforms share a Seller Central login but have entirely different payment flows, fee structures, and reconciliation procedures.

This article covers Amazon Pay (the payment gateway) exclusively.

What Makes Amazon Pay Reconciliation Different From Other Gateways?

Amazon Pay's reconciliation has four characteristics that make it harder than PayPal or Stripe and require careful attention from bookkeepers and CPAs.

1. Settlement Timing Is Not Daily or Weekly — It Is Activity-Driven

Amazon Pay does not disburse on a fixed daily or weekly schedule by default. A settlement occurs when Amazon Pay calculates your account balance across all recent transactions, deducts fees, reserves, and charges, and — if the balance is positive — initiates an ACH transfer to your bank account. This typically happens on a rolling basis, but Amazon Pay explicitly states that funds usually take 3 to 5 business days from settlement initiation to arrive in your bank account.

This creates a structural mismatch: the Settlement report date is not the bank deposit date. A settlement initiated on November 28 may appear in your bank account on December 2. For month-end close, this means a deposit arriving in December may belong to a November settlement — and the clearing account must absorb this timing difference cleanly.

2. Reserves Held Against Your Balance

Amazon Pay enforces a reserve policy on merchant accounts, particularly for newer merchants or those with elevated chargeback or refund rates. Reserves are funds withheld from disbursement and held as a security buffer against potential claims or chargebacks. They appear in your settlement report as a deduction from Available Funds and remain in the closing balance of your Amazon Pay account until released.

Key reserve terms from Amazon Pay's official definitions:

• Account Reserve: Funds in your account that will not be disbursed within the selected settlement period, used to cover potential claims or chargebacks.

• Beginning Balance: The amount withheld as account reserve from the previous statement, plus any amount carried over from the previous balance.

• Carryover: A credit or debit from the un-disbursed account balance of a specific settlement period.

• Unavailable Balance: The amount not available for payout due to reserves, debt, or other reasons.

Reserves mean your Amazon Pay closing balance is almost never $0 — even after all payouts have been received. This is a critical difference from Shopify or Stripe, where the clearing account typically shows $0 after all payouts are disbursed. For Amazon Pay, your Amazon Pay Bank Account clearing in QBO will consistently carry a non-zero balance equal to the reserve held by Amazon.

3. Fees Are Bundled Under "Expenses" — Not Separated by Default

Amazon Pay's Statement View groups all fees under one line item called Expenses, which includes: processing fees, cross-border fees, authorization fees, chargeback fees, and any applicable provider fees. In the Transaction View (the detailed CSV), these break out into individual columns — but the Statement PDF only shows the aggregate.

For QBO bookkeeping, this means you must use the Transaction Report (CSV) to get line-item fee detail. If you rely only on the Statement PDF, you cannot separate processing fees from chargeback fees or cross-border fees in your P&L.

4. Amazon Pay Is a Pure Payment Gateway — No Sales Data

Amazon Pay processes payment authorization and capture. It does not know your product names, SKUs, product categories, or sales tax rates. The settlement report contains order amounts and fees — nothing else. For sales tax, product-level income, and shipping detail, you must cross-reference your ecommerce platform's order reports (Shopify, WooCommerce, BigCommerce, etc.).

This means Amazon Pay reconciliation is always a two-source exercise: the Amazon Pay Settlement Report (for payout amounts and fees) plus your ecommerce platform's order report (for sales tax, product breakdown, and shipping). PayTraQer handles the Amazon Pay side; your ecommerce platform connector handles the order side.

5. Individual Sync Only — No Summary/Consolidated Mode

PayTraQer syncs Amazon Pay transactions in individual (itemized) mode. Unlike some gateways where you can choose between one summary entry per payout versus individual entries per transaction, Amazon Pay always creates one QBO Sales Receipt per captured transaction. This means:

• A merchant with 300 Amazon Pay orders per month will see 300 Sales Receipts in QBO plus the corresponding fee and refund entries.

• Reconciliation requires matching the aggregate of all those individual entries to the Amazon Pay settlement report totals.

• The clearing account balance must tie to the sum of all open individual entries plus reserve, not to a single summarized payout entry.

Understanding Amazon Pay Transaction Types

Amazon Pay's official reporting term definitions document identifies these transaction types, all of which PayTraQer maps into QBO:

Amazon Pay Transaction Types

How the Settlement Report Groups These Transactions

The Amazon Pay Settlement Report has two views:

Statement View (PDF — overview):

• Beginning Balance (prior reserve carryover)

• Income (sum of all captures)

• Expenses (sum of all fees — processing, cross-border, auth, chargeback fees)

• Refunds (sum of all refunds + A-to-z claims)

• Account Reserve (funds withheld this period)

• Available Funds (what is disbursed)

• Transfer (amount sent to your bank)

• Closing Balance (reserve carried into next period)

Transaction View (CSV — detail):

• One row per transaction

• Columns: Settlement ID, Transaction Type, Order Reference ID, Seller Order ID, Capture ID, Seller Reference ID, Transaction Amount, Total Fee (TransactionPercentageFee + TransactionFixedFee), Transaction Date, PaymentType, OrderType, Channel

The CSV Transaction View is the source of truth for QBO reconciliation. The Statement PDF provides high-level totals to verify against.

How PayTraQer Syncs Amazon Pay to QBO

PayTraQer connects to Amazon Pay via API credentials entered in Seller Central and downloads all transaction-level data from the Transaction View. The individual sync model works as follows:

1. For each Capture transaction: PayTraQer creates one Sales Receipt in QBO, deposited to your Amazon Pay Bank Account clearing account.

2. For each fee (processing, cross-border, authorization, chargeback fee, misc.): PayTraQer creates an Expense entry with the corresponding expense account, deducted from Amazon Pay Bank Account.

3. For each Refund: PayTraQer creates a Refund Receipt or Credit Memo in QBO, reducing Amazon Pay Bank Account.

4. For each A-to-z Claim or Chargeback: PayTraQer creates an Expense entry deducted from Amazon Pay Bank Account.

5. When Amazon Pay initiates a disbursement: PayTraQer creates a Bank Transfer from Amazon Pay Bank Account → Checking Account for the net disbursed amount.

6. The Reserve portion of the balance stays in Amazon Pay Bank Account — it is not transferred and is not reconcilable against a bank deposit. It is the non-zero closing balance of the clearing account.

Because PayTraQer uses individual sync only for Amazon Pay, the Amazon Pay Bank Account register in QBO will contain one Sales Receipt per order, individual fee entries, and individual refund entries — rather than aggregated journal entries. This is the expected behavior and is how the reconciliation works: the sum of all individual entries ties to the settlement report totals.

Step 1 — Prerequisites and QBO Chart of Accounts Setup

Complete this entire step before opening PayTraQer. Setting up the correct chart of accounts is what makes every downstream reconciliation accurate and clean.

Create the Amazon Pay Clearing Account

1. QBO → Accounting → Chart of Accounts → New

2. Account Type: Bank

3. Detail Type: Checking

4. Name: Amazon Pay Bank Account

5. Currency: USD (or your operating currency)

6. Save and Close.

Why Bank type, not Other Current Asset? Bank type is required for two reasons: (1) it enables QBO's Reconcile function so you can reconcile this account against the Amazon Pay Settlement Report, and (2) it enables the Banking tab to recognize and match Bank Transfers (the mechanism PayTraQer uses for disbursements). Other Current Asset accounts cannot be reconciled through Accounting → Reconcile.

Important: This account must be used exclusively for Amazon Pay transactions. Do not use this account for any other payment gateway or income source. If the same clearing account receives transactions from multiple sources, your reconciliation will fail every single month.

Create Amazon Pay-Specific Income and Expense Accounts

Before mapping anything in PayTraQer, create these accounts in your QBO Chart of Accounts:

Note on A-to-z Claims vs. Chargebacks: These are two distinct dispute mechanisms in Amazon Pay and must be tracked separately. A-to-z Claims are Amazon's own buyer protection program — Amazon resolves them internally and debits your account. Chargebacks are initiated at the card issuer level and go through the card network. Chargeback fees ($20 each) only apply to chargebacks, not to A-to-z Claims.

Download Your Amazon Pay Source of Truth Reports

From Seller Central → Reports → Payments:

1. The Settlement Report (Transaction View CSV) — Your Primary Reconciliation File

• In Seller Central: Reports → Payments → Date Range Reports tab

• Create a new Date Range Settlement report

• Select report type: Transaction (not Summary)

• Set date range: first day to last day of the month

• Click Generate → wait for it to appear → Download

• Open in Excel or Google Sheets

This CSV file contains every Amazon Pay transaction for the period, one row per transaction. This is what you compare against PayTraQer's synced entries in QBO line by line.

2. The Statement View (PDF) — Your Verification Totals

• In Seller Central: Reports → Payments → All Statements tab

• Download the statement covering your reconciliation period

• Note these five figures for use during QBO reconciliation:

  • Beginning Balance (prior reserve carryover)

  • Income (total captures)

  • Expenses (total fees — all types)

  • Refunds (total refunds + A-to-z claims)

  • Closing Balance (this is your Amazon Pay Bank Account ending balance for QBO reconciliation)

  • Transfer amount (this is the bank deposit you match in QBO banking)

3. Bank Statement or Bank Feed

• Confirm the Amazon Pay ACH deposit amount and date in your real bank statement

• Amazon Pay ACH deposits appear as "AMAZON PAYMENTS" in most bank feeds

• Note: the deposit date in the bank is 3–5 business days after the settlement initiation date shown in the report

Step 2 — Connecting Amazon Pay to PayTraQer

Obtain Amazon Pay API Credentials

PayTraQer connects to Amazon Pay using API credentials from Seller Central. Before connecting:

1. Sign in to Seller Central

2. Go to Settings → User Permissions

3. Under Third-party developer and apps, click Visit Manage Your Apps

4. Find PayTraQer in the apps list (or authorize PayTraQer to access your account)

5. Confirm the API connection grants access to Payments reports and transaction data

Connect Amazon Pay in PayTraQer

1. Log in to PayTraQer

2. Go to Connectors → + Add New → Payment Platforms

3. Select Amazon Pay

4. Enter your Amazon Pay Merchant ID and MWS Auth Token (or authorize via OAuth if using the newer Selling Partner API method)

5. Test the connection — PayTraQer will confirm successful access to your Amazon Pay transaction data

6. Click Save

Step 3 — Configuring PayTraQer Settings for Amazon Pay

In PayTraQer → Settings → Amazon Pay. Work through each settings section in this exact order before running any sync.

Sales Settings

• Bank Account to Deposit: Amazon Pay Bank Account (your clearing account — NOT your Checking account)

• Income Account: Amazon Pay Sales

• Payment Method: Amazon Pay

• Customer: Common Customer (Amazon Pay Customer) — recommended for most merchants. PayTraQer will use one generic customer for all Amazon Pay orders, keeping QBO's customer list clean.

  • Exception: If you need per-customer records in QBO for warranty, subscription management, or B2B invoicing through Amazon Pay, switch to customer matching by buyer email or Order Reference ID.

• Class / Location Tracking: If your QBO company uses Class or Location tracking, assign Amazon Pay as a class here so all Amazon Pay income and fees can be filtered in P&L by class.

Key rule: The Bank Account in Sales Settings must always be Amazon Pay Bank Account. If it is accidentally set to your Checking Account, PayTraQer will post each Sales Receipt directly to Checking — bypassing the clearing account entirely. The clearing account will be empty, bank feed matching will be impossible, and income will be double-recorded when deposits arrive.

Tax Settings

Amazon Pay is a pure payment gateway — it does not collect or report sales tax. The transaction amount in the Amazon Pay report is the gross order amount as charged by your ecommerce platform, which may or may not include tax depending on how your platform handles it.

Tax handling in PayTraQer for Amazon Pay:

• If your ecommerce platform collects tax (e.g., Shopify collects and remits tax on your behalf): The Amazon Pay capture amount includes the gross order total with tax. In PayTraQer, map the tax portion to your Sales Tax Payable account — but verify the tax amount against your ecommerce platform's order report, since Amazon Pay's settlement report does not itemize tax separately.

• If you self-collect tax outside the Amazon Pay flow: Leave tax mapping in PayTraQer at the full order amount in Amazon Pay Sales. Handle tax recording via your ecommerce platform's connector.

• If tax is not in the Amazon Pay capture at all (common in B2B or digital goods): No tax mapping needed in PayTraQer.

Best practice: For most Shopify + Amazon Pay setups, configure tax mapping in your Shopify connector (not in PayTraQer's Amazon Pay connector) since Shopify has the complete tax breakdown. In PayTraQer, set the full Amazon Pay capture amount to Amazon Pay Sales.

Fees Settings

Map each Amazon Pay fee type individually. This is where most CPA configurations fail — lumping all fees into one "Processing Fees" account loses the detail needed to understand your true cost per transaction type.

Critical Rule: The Bank Account for every single fee type must be set to Amazon Pay Bank Account — the same clearing account used in Sales Settings. Every dollar that moves in Amazon Pay's ledger (income or expense) must pass through the clearing account. If any fee is pointed to a different account, the clearing account will not balance against the settlement report.

Payout / Disbursement Settings

• Enable "Process the Payout": Toggle ON

• Transfer Account: Your real Business Checking Account

• Negative Balance Account: Business Checking Account

When "Process the Payout" is ON, PayTraQer detects each Amazon Pay disbursement and creates a Bank Transfer from Amazon Pay Bank Account → Checking Account for the exact disbursed amount. This Bank Transfer is what QBO matches to the ACH deposit in your bank feed.

The Negative Balance Account handles the rare but real situation where Amazon Pay's balance goes negative — typically when refunds and fees exceed captures in a settlement period. Amazon Pay will charge your payment method on file and credit your account (Balance Repayment). PayTraQer records this as a reverse Transfer: FROM Business Checking Account TO Amazon Pay Bank Account. Configure the Negative Balance Account to your Business Checking Account.

Refund Settings

• Refund Account: Amazon Pay Refunds

• Bank Account for Refunds: Amazon Pay Bank Account

Full refunds reverse the original capture amount and may also reverse part of the processing fee (Amazon Pay refunds the non-fixed portion of the fee on full refunds). Map refunds to the Amazon Pay Refunds contra-revenue account so they reduce gross sales on your P&L rather than appearing as an expense.

Step 4 — Syncing Amazon Pay Transactions Into QBO

Understanding the Individual Sync Model

Because PayTraQer uses individual (itemized) sync for Amazon Pay — not summary/consolidated mode — each sync produces:

• One Sales Receipt per Capture — posted to Amazon Pay Bank Account

• One Expense entry per fee deduction — posted to Amazon Pay Bank Account

• One Refund Receipt per Refund — posted to Amazon Pay Bank Account

• One Expense entry per A-to-z Claim or Chargeback — posted to Amazon Pay Bank Account

• One Bank Transfer per Disbursement — FROM Amazon Pay Bank Account TO Checking Account

For a merchant processing 200 Amazon Pay orders per month, the Amazon Pay Bank Account register in QBO will show approximately 400–600 line items (200 sales receipts + ~200 fee lines + any refunds, disputes, and transfers). This is normal and expected. Do not attempt to consolidate or summarize these manually — they are the individual audit trail that matches the Transaction View CSV row for row.

Initial Sync Steps

1. In PayTraQer → Connectors → Amazon Pay → Transactions Dashboard

2. PayTraQer automatically downloads recent Amazon Pay transactions on first connection

3. For historical periods: use Download Historical Transactions → set custom date range → Download

4. Set your target period date range

5. In the Not Synced tab, all downloaded transactions appear for review

6. Before clicking Sync, review a sample of transactions to confirm:

   • Each Capture shows Amazon Pay Bank Account as the deposit account

   • Each fee shows the correct expense account and Amazon Pay Bank Account as the bank

   • Each Refund shows Amazon Pay Refunds as the account and Amazon Pay Bank Account as the bank

   • Each Disbursement shows a Bank Transfer to Checking Account

7. If settings look correct for all transaction types, click Sync to QuickBooks

Ignore/Skip Specific Transactions

PayTraQer allows you to select specific transactions and click Ignore/Skip if you do not want them in QBO. Use this for:

• Authorized but never captured transactions (these are not income and should not be in QBO)

• Cancelled orders that were never fulfilled

• Test transactions from sandbox/integration testing

Ignored transactions appear in the Ignored tab and can be resumed later if needed.

Verify in QBO After Sync

1. QBO → Accounting → Chart of Accounts → Amazon Pay Bank Account → View Register

2. You should see:

   • Individual Sales Receipts for each Capture

   • Fee expense entries for each fee type

   • Refund entries

   • Bank Transfers to Checking for each disbursement

   • A running balance that reflects: (Total Captures) - (Total Fees) - (Total Refunds) - (Total Disbursements) = Current Reserve Balance in Amazon Pay

3. The current balance in the Amazon Pay Bank Account QBO register should approximately equal the Closing Balance on your Amazon Pay Statement View PDF (the reserve Amazon is holding). It will not be $0.

Enable Auto-Sync

After confirming the initial sync is accurate: PayTraQer → Settings → Automation → Enable Auto-Sync. PayTraQer will then automatically pull new Amazon Pay transactions and post them to QBO as they occur, without manual downloads.

Step 5 — The QBO Bank Feed Matching Process

When Amazon Pay's ACH transfer arrives in your bank account (3–5 business days after the settlement initiation date):

1. QBO → Banking → Banking → For Review (your Checking Account)

2. Find the Amazon Pay deposit — it appears as "AMAZON PAYMENTS" or "AMZN PAY" in the payee column

3. Because PayTraQer created a Bank Transfer from Amazon Pay Bank Account → Checking Account for this exact disbursed amount, QBO will highlight it in green and suggest a Match

4. Click Match

Never click "Add." Clicking Add records the Amazon Pay disbursement as new income directly in your Checking Account — completely duplicating all the Sales Receipts that PayTraQer already posted to Amazon Pay Bank Account. This is the primary double-counting error for Amazon Pay in QBO.

What If the Match Amount Is Off?

If the Amazon Pay ACH deposit in your bank does not match the PayTraQer Bank Transfer amount, the most common causes are:

• Reserve change: Amazon Pay increased or decreased your reserve between settlement initiation and disbursement. Check the Statement View for the difference between Available Funds and the actual Transfer line.

• Timing difference: The disbursement straddles a period boundary. PayTraQer may have logged the transfer in the previous period. Expand the date range in QBO's Match window to look further back.

• Balance Repayment charged: Amazon Pay charged your card on file for a negative balance, which then affected the net disbursement amount. Check for a Balance Repayment transaction type in the CSV.

• Multiple settlements in one ACH: In some account configurations, Amazon Pay batches multiple settlement periods into one bank transfer. If this occurs, the bank deposit amount will equal the sum of two PayTraQer Bank Transfer entries. In QBO, click Match and select both Bank Transfers to match against the single deposit.

Creating a QBO Bank Rule for Amazon Pay Deposits

For ongoing efficiency:

1. QBO Banking → Rules → New Rule

2. Condition: Bank text contains "AMAZON PAYMENTS" (or "AMZN PAY" — check your actual bank feed label first)

3. Action: Transfer from Amazon Pay Bank Account

This pre-categorizes future Amazon Pay deposits as Transfers, reducing each match to a single confirmation click.

Step 6 — Reconciling the Accounts in QBO

Reconcile the Amazon Pay Bank Account (Clearing Account) — The Critical Step

This is the reconciliation that most bookkeepers skip or do incorrectly for Amazon Pay. Because the closing balance of Amazon Pay Bank Account is not $0 (due to reserves), the reconciliation requires the correct ending balance number from the Amazon Pay Statement.

1. QBO → Accounting → Reconcile

2. Select account: Amazon Pay Bank Account

3. Ending Balance: Enter the Closing Balance from your Amazon Pay Statement View PDF for the period end date. This is the reserve amount Amazon Pay is holding — it is the money that remains in your Amazon Pay account after all disbursements have been made.

   • Example: If Amazon Pay disbursed $8,400 and is holding $600 in reserve, the Closing Balance is $600. Enter $600.00 as the Ending Balance.

4. Ending Date: Last day of the month

5. Click Start Reconciling

6. Check off:

   • All Sales Receipts (Captures) — tick each one

   • All Fee Expense entries — tick each one (processing fees, cross-border fees, auth fees, chargeback fees, misc fees)

   • All Refund entries — tick each one

   • All A-to-z Claim and Chargeback expense entries — tick each one

   • All Bank Transfers to Checking (disbursements) — tick each one

   • Do not tick any pending reserve transactions that have not yet been released

7. Difference must read $0.00

8. Click Finish Now → save the reconciliation report PDF

Understanding Why the Ending Balance Is Not $0

For every other gateway in this article series (Shopify, Stripe, eBay, PayPal), the clearing account typically shows an ending balance of $0 after all payouts are received — or a small in-transit amount if a payout was initiated near month-end.

Amazon Pay is different. The reserve is a permanent, ongoing balance that Amazon holds for risk management purposes. It is not in-transit — it has been withheld deliberately. The correct QBO reconciliation for Amazon Pay:

• Amazon Pay Bank Account ending balance = Amazon Pay Closing Balance (reserve amount)

• All disbursements have been transferred to Checking

• All captures, fees, refunds, and claims have been ticked off

• The remaining unticked balance equals the reserve

If Amazon Pay releases part of the reserve next month, that release will appear as an addition to next month's Available Funds, which gets disbursed — and you will reconcile next month's clearing account to the new (lower) Closing Balance.

Verify Against Statement View Totals

Before clicking Finish Now, cross-check the QBO reconciliation screen against your Amazon Pay Statement PDF:

If any row does not match, do not click Finish Now. Instead, return to PayTraQer's Transactions Dashboard, check the Error tab for any failed syncs, and re-sync the missing transactions.

Reconcile the Main Checking Account

After completing the Amazon Pay Bank Account reconciliation, proceed with your standard bank reconciliation. All matched Amazon Pay ACH transfers will appear as cleared items.

Handling the Reserve: A Detailed Walkthrough

The reserve is the single most confusing aspect of Amazon Pay reconciliation for bookkeepers who are new to the platform. Here is a concrete example showing how it flows through QBO over two months.

Example: November to December Reserve Flow

End of November:

• Total Captures (Income): $10,000

• Total Fees (Expenses): -$290

• Total Refunds: -$400

• Disbursed to bank: $8,710 (Bank Transfer created by PayTraQer)

• Reserve held by Amazon Pay: $600 (Closing Balance = $600)

QBO November reconciliation of Amazon Pay Bank Account:

• Tick all Sales Receipts totaling $10,000

• Tick all Fee entries totaling $290

• Tick all Refund entries totaling $400

• Tick the Bank Transfer of $8,710

• Ending Balance: $600 ← from Amazon Pay Statement Closing Balance

• Difference: $0.00 ✓

Beginning of December:

• Amazon Pay Beginning Balance: $600 (the prior reserve carries forward)

• PayTraQer does NOT create any new QBO entry for this carryover — the $600 is already in Amazon Pay Bank Account from November's reconciliation

During December:

• New Captures: $12,000 (new Sales Receipts in QBO)

• New Fees: -$348

• New Refunds: -$500

• Amazon Pay releases $200 of the prior reserve (your account is in good standing)

• Disbursed to bank: $11,552 ($600 prior reserve release + $12,000 - $348 - $500 - $200 new reserve held = $11,552)

• New reserve: $200

QBO December reconciliation of Amazon Pay Bank Account:

• Beginning Balance: $600 (carried from November)

• Tick all new Sales Receipts: $12,000

• Tick all new Fee entries: $348

• Tick all new Refund entries: $500

• Tick the Bank Transfer of $11,552

• Ending Balance: $200 ← from December Amazon Pay Statement Closing Balance

• Difference: $0.00 ✓

Common Amazon Pay-Specific Scenarios and Fixes

Amazon Pay + Your Ecommerce Platform: The Two-Source Reconciliation

Because Amazon Pay reports only payment captures and fees — not product names, sales tax, or shipping breakdowns — a complete bookkeeping setup requires reconciling two data sources together:

For Shopify + Amazon Pay

Configuration note: In your Shopify connector, the Amazon Pay orders should be routed to the Amazon Pay Bank Account clearing account — not to a Shopify Payments Clearing account. This ensures that the Shopify order data (for product/tax detail) and the Amazon Pay payment data (for capture/fee detail) both point to the same clearing account. The individual QBO Sales Receipts created by PayTraQer from the Amazon Pay side serve as the payment records; the Shopify side provides the product and tax line items.

Avoid double-counting: If both PayTraQer's Shopify connector AND PayTraQer's Amazon Pay connector are creating Sales Receipts for the same orders, you will double-count income. Configure your Shopify connector to skip Amazon Pay orders (or skip creating Sales Receipts for orders paid via Amazon Pay), and let the Amazon Pay connector handle all payment recording for those orders.

For WooCommerce + Amazon Pay

Same principle: use your WooCommerce connector for product/order data and the Amazon Pay connector for payment capture and fee data. Ensure both connectors point Amazon Pay orders to the same Amazon Pay Bank Account clearing account.

Final Month-End Checklist for Amazon Pay + QBO Reconciliation

•  Amazon Pay Date Range Settlement Report (Transaction View CSV) downloaded from Seller Central

•  Amazon Pay Statement View PDF downloaded — Closing Balance noted for reconciliation ending balance

•  Amazon Pay Payouts/Disbursements confirmed in bank statement — ACH dates and amounts recorded

•  All Amazon Pay transactions confirmed "Synced" in PayTraQer Transactions Dashboard — Error tab is empty

•  Fee mappings verified: Processing, Cross-Border, Authorization, Chargeback, Misc fees all pointing to Amazon Pay Bank Account

•  A-to-z Claims mapped to Amazon Pay A-to-z Claims expense — not revenue

•  Chargeback fees ($20 each) in QBO — count matches number of disputes in CSV

•  Each Amazon Pay ACH deposit Matched (not Added) in QBO Banking For Review

•  Negative balance / Balance Repayment handled if applicable — reverse Transfer confirmed in QBO and bank

•  QBO Amazon Pay Bank Account register cross-checked: Total Captures vs. CSV Income total; Total Fees vs. CSV Expenses total; Total Refunds vs. CSV Refunds total; Total Bank Transfers vs. CSV Transfer amount

•  Amazon Pay Bank Account clearing reconciled — Ending Balance = Amazon Pay Statement Closing Balance — Difference $0.00

•  P&L reviewed: Amazon Pay Sales shows gross captures; fee accounts show individual fee types; refunds reduce income correctly

•  Balance Sheet reviewed: Amazon Pay Bank Account balance equals current Amazon Pay reserve (not $0)

•  Ecommerce platform connector (Shopify/WooCommerce/BigCommerce) confirmed not double-counting Amazon Pay orders

•  Reconciliation PDF saved to client folder