February 10, 2025
PayTraQer is an e-commerce accounting automation application by SaasAnt that automatically syncs sales, fees, refunds, and payouts from your online platforms and payment processors into QuickBooks Online or Xero. Instead of manually entering transactions from every channel you sell on, PayTraQer fetches and categorizes that data for you, keeping your books accurate without the manual work.
Video Tutorial for How to Set Up PayTraQer in QuickBooks Online for E-commerce Bookkeeping:
If you sell online across multiple platforms — say Shopify, Amazon, eBay, Walmart, and others or collect payment using platforms like PayPal, Stripe, or Square simultaneously — you're receiving deposits from each one at different times, with fees and taxes deducted differently by each. Recording all of this manually into QuickBooks is slow, error-prone, and gets harder the more you sell. PayTraQer automates the entire process: fetch, categorize, map to the right accounts, and post, so your books stay current without manual entry.
PayTraQer is built for:
E-commerce sellers on Shopify, Amazon, eBay, WooCommerce, Walmart, Squarespace, BigCommerce or Etsy who want their sales automatically in QuickBooks or Xero
Business owners accepting payments via PayPal, Stripe, Square, or Clover who are tired of manually reconciling deposits
Bookkeepers and accountants managing clients with multiple sales channels who need clean, matched deposits without manual work
Growing businesses moving from spreadsheets to proper accounting software and needing a clean automated sync setup
PayTraQer works with QuickBooks Online and Xero.
No. PayTraQer is made by SaasAnt. It is an officially listed and Intuit-trusted app in the QuickBooks App Store.
PayTraQer integrates with:
E-commerce platforms: Amazon, Shopify, eBay, WooCommerce, BigCommerce, Ecwid, Etsy, Walmart, Squarespace
Payment processors: PayPal, Stripe, Square, Clover, Authorize.Net, Braintree, Amazon Pay, Pin Payments
Accounting software: QuickBooks Online, Xero
Yes. You can connect all your sales channels and payment processors simultaneously to one QuickBooks or Xero company. For example, Shopify + Stripe + PayPal + Amazon can all sync into the same QBO file, with each platform posting to its own designated account.
Yes. PayTraQer syncs Shopify sales, refunds, taxes, shipping, and payout deposits into QuickBooks or Xero. You can assign separate income accounts for Shopify to track it independently from your other sales channels.
Yes. PayTraQer connects to PayPal and syncs sales, fees, refunds, and payouts directly into QuickBooks or Xero. You can assign dedicated income and expense accounts for PayPal to keep it clearly separated in your books.
Yes. PayTraQer syncs Stripe payments, processing fees, refunds, and payout deposits to QuickBooks or Xero. Stripe processing fees are automatically identified and posted to your configured expense account so your net revenue is accurately reported.
Yes. PayTraQer syncs Square sales, daily deposits, refunds, and processing fees to QuickBooks or Xero. This includes both in-person Square POS transactions and online Square payments.
Yes. PayTraQer connects to Amazon Seller Central and syncs your settlement data — including sales, refunds, FBA fees, advertising charges, and marketplace facilitator tax — into QuickBooks or Xero. Amazon data syncs based on settlement periods, not individual order dates, which matches how Amazon actually pays you.
Yes. PayTraQer supports eBay Managed Payments and syncs eBay payout data to QuickBooks or Xero.
Yes. PayTraQer integrates with WooCommerce stores and syncs sales, fees, taxes, and refunds to QuickBooks or Xero. WooCommerce transactions can be mapped to separate income accounts for clean multi-channel reporting.
Yes. PayTraQer syncs BigCommerce sales, fees, refunds, and expenses automatically on autopilot, including transactions from payment gateways connected to your BigCommerce store.
Yes, but Amazon Pay is a separate connection from Amazon Seller Central. Amazon Pay connects independently in PayTraQer and can be mapped to its own QBO or Xero accounts for sales, service fees, and refunds.
Yes. PayTraQer can simultaneously sync Shopify order data and Stripe payout data into the same QuickBooks or Xero company. You configure separate income and fee accounts for each so your Shopify sales and Stripe processing fees are tracked independently, giving you a clean view of revenue by channel.
Yes. PayTraQer is specifically designed for multi-channel sellers. Both PayPal and Amazon can be connected to the same PayTraQer account and post to the same QuickBooks company, with each platform using its own account mapping so nothing gets mixed together.
Yes. PayTraQer supports multiple QuickBooks or Xero companies under one login. Each company has its own separate settings, platform connections, account mappings, and subscription. Your clients can invite you as a user without sharing their login credentials.
Yes. PayTraQer lets you set a custom historical start date and import transactions going back as far as each platform's API allows. Set the date range, let PayTraQer fetch the historical data, configure your account mappings, and then sync it into QuickBooks in one batch.
PayTraQer is the bridge between your sales platforms and your accounting software. Once connected and configured, it handles the fetch-categorize-sync cycle automatically. You review transactions in the PayTraQer dashboard, confirm the mapping looks right, and click sync — or enable auto-sync to run on a schedule without any manual action.
PayTraQer works well for Stripe-based businesses including subscriptions. It syncs Stripe charges, refunds, and payouts to QuickBooks or Xero. For businesses with complex revenue recognition needs (deferred revenue, multi-period contracts), evaluate whether Summary Sync or Itemized Sync better matches your accounting method, and confirm the approach with your accountant.
Yes. Both Square and Shopify can be connected simultaneously to the same QuickBooks company through PayTraQer. You assign separate income accounts for each channel so your in-person and online revenue are tracked distinctly on your P&L.
There are two ways to install:
From QuickBooks Online: Apps → Find Apps → Search "PayTraQer" → Get App Now → Connect
From the SaasAnt website: Sign up at saasant.com, then connect your QBO or Xero company via OAuth
After installing, your first step is choosing a sync mode — the most important decision in your setup.
Before starting:
An active QuickBooks Online or Xero subscription
Master Admin or Accountant-level access to your accounting company (standard user access is not sufficient)
Active accounts on the platforms you want to connect (Shopify, Amazon Seller Central, Stripe dashboard, PayPal, etc.)
Your sync mode — either Summary Sync or Itemized Sync. This choice is made once, immediately after connecting your accounting software. It applies to all connected platforms and cannot be changed later without resetting your entire account. Read the sync mode section below before proceeding with setup.
Summary Sync | Itemized Sync | |
What posts | One journal entry per payout period | One entry per transaction |
Best for | Clean books, easy reconciliation | Transaction-level detail in QBO/Xero |
Volume in books | Low — one entry per deposit | High — hundreds of entries |
Reconciliation | Match payout total to bank deposit | Match each transaction individually |
Typical user | Most small-to-mid e-commerce sellers | Accountants needing granular records |
For most e-commerce businesses — especially those selling on multiple platforms — Summary Sync is the better default. It keeps your QuickBooks or Xero books clean with one journal entry per payout, which reconciles simply against your bank deposit. Use Itemized Sync only if your accountant specifically needs every individual transaction visible as a separate line in your accounting software.
No. Switching between sync modes is not directly feasible within the app. To switch, you must fully disconnect the PayTraQer app — which permanently erases all settings, profile data, account mappings, and subscription information — and then reinstall from scratch. This is why the sync mode decision must be made before setup begins.
In this order:
General Settings — default bank account, date range, auto-sync preference
Sales Settings — income account per platform
Tax Settings — tax liability account per platform
Fees & Expenses Settings — expense account per platform
Payout Settings (Summary Sync only) — confirm which bank account each platform's deposits go to
COGS Settings (optional) — only if you sell physical products and track inventory in QBO/Xero
Yes. PayTraQer supports per-platform account assignment for income, tax, and fees. You can post Shopify sales to "Shopify Revenue," Stripe fees to "Stripe Processing Fees," and PayPal sales to "PayPal Income" — all as separate accounts in your chart of accounts.
A clearing or transit account is an intermediate account that receives payout entries before being matched to your actual bank account. Some accountants prefer this for a cleaner audit trail. If your accountant hasn't recommended it, posting directly to your business bank account is the simpler approach for most users.
Platforms like Amazon, Shopify, and others collect sales tax on your behalf in many jurisdictions. PayTraQer lets you map collected tax amounts to a QBO or Xero liability account (e.g., "Sales Tax Payable") per platform. For marketplace-remitted taxes where the platform files directly with the government, configure this as a pass-through entry so the liability nets to zero in your books.
From the Transactions Dashboard:
Filter by date range, platform, and "Not Synced" status
Select transactions
Click Preview — confirm the accounts, amounts, and descriptions look right
Click Sync — PayTraQer posts the entries to your accounting software
Verify in QBO or Xero that the income, fees, and bank accounts reflect the right amounts
Preview shows you exactly how a transaction will post to QuickBooks or Xero — which accounts will be debited and credited, the amounts, and the description — before anything is committed. Always preview a small batch of 3–5 transactions before running your first bulk sync. It is the fastest way to catch a wrong account mapping before it reaches your books.
Auto-sync posts new transactions on a schedule without any manual action. Enable it only after you have confirmed your account mappings are correct through at least one successful manual preview-and-sync cycle. Turning it on before validating settings means errors will post to QBO automatically.
Yes. Set a custom start date in General Settings and PayTraQer will fetch available historical data from each connected platform. The amount of history available depends on each platform's API retention.
Yes. Select any transaction in the dashboard and click Exclude. Excluded transactions won't post to your accounting software and won't appear in your unsync count. Use this for test transactions, personal transfers, or anything already recorded manually.
After syncing:
Open QuickBooks Online and go to your bank account register
Find the PayTraQer journal entry for the payout period
Match it to the actual bank deposit from the platform
The net amount on the journal entry should equal the bank deposit amount exactly
If they match — reconciliation is complete
Common causes:
A fee type is not mapped in your Fees & Expenses Settings and is being dropped
Tax is being included or excluded inconsistently
A refund processed in a different payout period than expected
Reserved or pending balance amounts withheld by the platform
A date mismatch — the platform deposits 1–2 days after the payout cycle closes
The most common reason is a date basis difference. Your platform report may show sales by transaction date while PayTraQer posts by payout/settlement date. Always compare using payout or settlement view in your platform's reporting — not order date view.
At month-end:
Confirm all payouts for the month have synced in PayTraQer (no "Not Synced" entries remaining)
In QBO or Xero, match each PayTraQer entry to its corresponding bank deposit
Verify income, fee, and tax account balances against your platform payout reports
Lock the period in your accounting software once reconciliation is confirmed
Check in order:
Platform connection is still active — re-authorize if needed
Date range filter is set to include the period you're looking for
Historical data download has been triggered for older transactions
The connected account is the correct one, not a test or secondary account
Error means PayTraQer tried to post but QBO or Xero rejected it. Common causes:
A mapped account was renamed or deleted in QBO/Xero
A required field is missing (customer name, tax rate)
The QBO/Xero OAuth connection has expired — reconnect in Settings → Connections
Currency mismatch between the platform and your accounting company
Duplicates happen when transactions were already entered manually in QBO, or when data was re-synced without rolling back the original sync first. Roll back the PayTraQer-synced entries using "Undo Sync," delete the manual duplicates in QBO, then re-sync with Preview enabled.
From the Transactions Dashboard:
Filter by Status: Synced
Select the transactions to undo
Click Undo Sync (selected) or Undo All (everything)
Confirm — PayTraQer removes those entries from QBO/Xero and resets them to "Not Synced"
"Undo All" removes every entry PayTraQer has ever posted to your accounting software. Only use this if you are starting completely fresh.
Yes. PayTraQer supports multi-company management from one login. Each company has its own platform connections, settings, and subscription. Bookkeepers and accountants use this to manage all their clients from a single dashboard.
Yes. PayTraQer handles multi-currency businesses by applying the exchange rate each platform uses during the payout. Set your base currency in General Settings. Multi-currency reconciliation requires QuickBooks Online Plus or Advanced (or the equivalent Xero plan).
You can connect a platform (e.g., Shopify) to different PayTraQer accounts tied to different QuickBooks companies. You cannot, however, connect the same platform account to two separate QBO companies simultaneously — each platform connection maps to one accounting company at a time.
Go to Settings → Users → Invite User, enter their email, and assign them a role. They receive an email invite and log in with their own credentials — you never need to share your password.
Admin users have full access including settings, connections, account mapping, and billing. Standard users can view and sync transactions but cannot change settings, disconnect platforms, or manage the subscription. Assign Standard role to team members who only need to run syncs.
PayTraQer offers a free trial. After the trial, a paid subscription is required based on your monthly transaction volume. You subscribe from within the app under the billing section.
Cancelling your subscription retains your data during a grace period. Disconnecting a platform connector removes your settings and mapping for that connector. Disconnecting all connectors — required to switch sync modes — resets your entire account: settings, history, and all mapping are permanently erased.
Plans are tiered by monthly transaction volume, not by the number of platforms connected. One plan covers all your connected channels.
Yes. PayTraQer includes COGS matching for businesses that sell physical products and track inventory in QuickBooks or Xero. You link inventory items in QBO/Xero to the products sold on your connected platforms, and PayTraQer creates COGS entries automatically when a sale syncs.
If your inventory is set up and managed in QBO or Xero natively, use PayTraQer's COGS matching. If you use a dedicated inventory tool (Cin7, Linnworks, InventoryLab, etc.) that already posts COGS to QBO, do not also enable PayTraQer's COGS feature — you will get duplicates.
The Analytics Dashboard gives a read-only financial overview across all connected platforms — total sales, fees, refunds, and payouts for any date range, with weekly, monthly, quarterly, and yearly breakdowns and per-platform comparisons. It also tracks new customers, average revenue per customer, and successful payments over time.
No. The Analytics Dashboard is a high-level monitoring tool for spotting trends across your platforms. For P&L statements, balance sheets, tax reports, or accountant-grade financials, use your accounting software's native reporting after syncing and reconciling through PayTraQer.