How to integrate Shopify with QuickBooks Online using SaasAnt PayTraQer

PayTraQer connects your Shopify store to QuickBooks Online. It syncs orders, refunds, fees, and payouts using your rules so deposits match and reports stay accurate.

Who this is for

• Bookkeepers and accountants supporting Shopify stores

• Store owners who want clean books without manual entry

• Teams comparing sync tools and looking for a safe first setup

Before you start

• An active QuickBooks Online company

• QuickBooks Online login with admin access

• Your Shopify admin credentials

• Optional: access for payment processors used in Shopify (Shopify Payments, PayPal, Stripe)

Quick setup: 5-minute success path

1. In QuickBooks Online, open Apps or Integrations, search PayTraQer, click Get app now, and authorize.

2. Choose Sync Mode: Consolidated (summary) or Itemized (one entry per order). Click Get Started.

3. In PayTraQer, go to Connectors → eCommerce connectors → Shopify → Connect, then sign in and approve.

4. Set Bank Account to deposit your sales/income to Shopify Bank Account. Save.

5. PayTraQer automatically downloads the last 60 days.

6. Turn on Auto Sync if you want PayTraQer to fetch and post new orders on a schedule.

7. In QuickBooks, verify one sale, one fee, and if enabled, one payout transfer.

Step by step Guide

1) Install PayTraQer from QuickBooks

• Open Apps or Integrations in QuickBooks Online

• Search PayTraQer and click Get app now

• Click Connect when prompted to allow access

• Enjoy the free trial to test your first sync

2) Choose your Sync Mode

You can change this later in settings. Test a short date range before switching.

3) Connect Shopify

• In PayTraQer, open Connectors → eCommerce connectors → Shopify → Connect

• Sign in to Shopify and approve access

• If you are not the admin, use Invite admin/client to send the authorization link

4) First-time settings

• Sales clearing bank: set Bank Account to deposit your sales/income to Shopify Bank Account per currency

• Payouts: decide if you want PayTraQer to create transfers to your checking account

• Save: PayTraQer auto-downloads the last 60 days

• Need other dates: use Download historical transactions with date filters

• Auto Sync: toggle on and set the interval to keep data flowing automatically

What the sync does

Notes

• Fees post to your fee expense account with vendor set to Shopify

• Payouts, when enabled, create a transfer that matches your bank deposit

Configure posting rules

Each section shows what it controls, a safe default, when to change it, and how to check.

Sales settings

Accounts

• Bank Account to deposit your sales/income

  • Default: Shopify Bank Account per currency

  • Change when: You keep separate clearing banks by currency or brand

  • Check: Sales and fees land in the same clearing bank

Payment method

• Payment methods to track your transactions

  • Default: Shopify

  • Check: Payment Method shows Shopify on created sales

Separate GL by payment system

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

  • Default: No

  • Use when: You link additional processors under Connectors → Payment connectors and want different GL routes per processor

  • Check: Posting accounts change based on the payment source

Record the Sales as

• Default: SalesReceipt

• Use when: Switch to Invoice if you bill first and collect later

• Check: New sales use the selected form

Customers

• Create Customer automatically if it does not exist

  • Default: Yes

  • Check: No missing customer errors

• Common Customer for your Sales Transactions

  • Default: Off

  • Use when: You run summaries or do not need per-customer detail

• Customize Customer Matching

  • Use when: Buyer names differ from QuickBooks

  • Check: Repeat buyers map to one customer record

Tracking

• Location/Department and Class

  • Your example: Location set to F05 - Events & Conferences; Class set to Administrative

  • General use: Pick your own Location and Class values if you track them

  • Check: New sales carry the selected values

Sync scope

• Skip the sales and process the associated fees only

  • Default: No

  • Use when: Sales are posted by another system and you only want fee expenses

Products and services Settings

Auto Creation

• Do you want to create Products/Services automatically

  • Default: No in your settings

  • Implication: Every item used by Shopify must already exist in QuickBooks, or you must use a Common Item

  • Tip: If you turn this On, choose the item Type for auto-created items

Type for auto-created items

• Default when enabled: Non-Inventory or Service

Income Account for auto-created items

• Default: Sales

• Check: New items point to the correct income account

Match Product

• Match Product by

  • Default: Name

  • Use when: Switch to SKU if both catalogs have stable SKUs

• Customize Product Matching

  • Use when: Names differ between Shopify and QuickBooks

  • Check: No duplicate items after sync

Common Item

• Use common product/service for all your sales

  • Default: No

  • Use when: You post summaries or do not need item detail

  • Then: Select common product/service to pick the default item

Tax settings

Auto Tax calculation

• Default: Yes to detect and apply tax on synced sales and expenses

Inclusive settings

• Tax Included in Payments

  • Enter the Tax Percentage (%) if your direct payments are tax-inclusive

• Shipping tax percentage

  • Enter the Tax Percentage (%) if shipping is taxable

Default Tax Code

• Tax Code

  • Choose a common code to apply to all transactions when required

  • This overrides automatic detection

• Check: Open a synced sale and confirm the tax code and amount

Fees settings

Core fee setup

• Vendor who receives the Payment Fees: set to Shopify

• Fee Category to record the expenses: choose Shopify Fees or your fee account

• Bank Account to record Payment Fees: Shopify Bank Account per currency

• Separate GL by payment system: keep No unless you want GL by processor

• Class and Location/Department for your Fees: set if you report by these fields

• Skip the fee details from syncing: keep No to capture fee lines

Payouts and settlements Settings

Do you want to process the payouts/settlements

• Default: No

• Turn On to create Bank Transfer transactions from the Shopify clearing bank to your checking account

• Check: Transfers match deposits in your bank feed when enabled

Clearing account vs checking account
The clearing account holds Shopify sales and fees inside QuickBooks.
The checking account is your real bank that receives the payout.
When payouts are on, transfers move money from clearing to checking so the clearing account nets to zero.

History and automation

• Download historical transactions: after first connect, pull other date ranges using the date filters

• Auto Sync: toggle on to download and post new transactions automatically at your chosen interval

Verify your first sync

Use a short date range, then check these in QuickBooks:

• A sale posts to the Shopify Bank Account with SalesReceipt and Payment Method Shopify

• Customer names follow your Customer Matching rules or your common customer

• Items exist and map correctly, or you used Common Item if you kept auto-create off

• One fee expense posts to Shopify Fees with vendor Shopify and the clearing bank

• The tax code and amount look right on a sample sale

• If payouts are on, a Bank Transfer moves funds to your checking account and matches your bank feed

Troubleshooting

• No data after connect
  Recheck Shopify authorization and connector status. Confirm date filters.

• Deposits do not match
  Turn on payouts and select your real checking account as the receiving account.

• Clearing account does not zero
  Post sales and fees to the same clearing bank and enable payouts.

• Wrong item on sales or duplicates
  Switch Match Product by to SKU or Name. Add Product Matching rules. Consider turning Auto-create items on.

• Duplicate customers
  Add Customer Matching rules or use a Common Customer for summaries.

• Tax looks off
  Review Auto Tax, Tax Included in Payments, Shipping tax, and Tax Code. Test again.

• Only need fee entries
  Turn on Skip the sales and process the associated fees only.

FAQs

Can I sync Shopify as a daily summary instead of itemized lines
Yes. Choose Consolidated during setup or change it later in Sync Mode.

How do I record Shopify fees to one expense account
In Fees settings, set vendor to Shopify and choose your fee expense account.

What form should I use for Shopify sales
Use Sales Receipts when payment is collected at checkout. Use Invoices if you bill first and collect later.

Can I bring in historic transactions
Yes. Use Download historical transactions with date filters.

Can I route different processors to different GL accounts
Yes. Link processors under Connectors → Payment connectors, then enable separate GL accounts by payment system.