BigCommerce QuickBooks Online Integration: Automated Accounting for BigCommerce Merchants

BigCommerce merchants who reconcile payouts manually in QuickBooks typically spend hours each month splitting gross order totals into revenue, fees, refunds, and tax. SyncTools eliminates that work by automating the entire data flow — from BigCommerce straight into QuickBooks Online, structured exactly the way your accountant expects.

TL;DR: SyncTools connects BigCommerce to QuickBooks Online — automatically syncing sales, refunds, payment gateway fees, shipping, taxes, and payout settlements into the correct QuickBooks accounts. Reconciles to your bank deposit exactly. Setup takes under 30 minutes.

Why BigCommerce Accounting Needs Automation

BigCommerce payouts bundle together sales revenue, payment gateway fees, refunds, and shipping income into a single deposit. Entering that correctly into QuickBooks requires breaking each payout into at least 6–8 line items and matching them against the corresponding bank transaction. Without automation, this work repeats every payout cycle.

SyncTools reads your BigCommerce transaction detail and creates properly structured QuickBooks records automatically — saving hours of manual work per month and eliminating the risk of coding errors that distort your P&L.

What SyncTools Syncs from BigCommerce to QuickBooks Online

Sales revenue — individual orders or summarized by day, week, or month
Refunds and returns — mapped to credit memo or refund receipt in QuickBooks
Payment processing fees — gateway fees as expenses against a dedicated QuickBooks account
Shipping income — separated from product revenue for accurate P&L reporting
Sales tax — mapped to correct QuickBooks tax liability accounts
Payout deposits — matched to bank transactions for one-click reconciliation
COGS — synced using BigCommerce product cost data for gross margin visibility

How to Set Up BigCommerce QuickBooks Online Integration

Step 1: Connect BigCommerce Log in to SyncTools and authorize the BigCommerce API connection. SyncTools requests read-only access to your store’s order and transaction data.

Step 2: Connect QuickBooks Online Authorize SyncTools via the QuickBooks Online OAuth flow. Map your BigCommerce revenue, expense, and tax categories to the corresponding QuickBooks chart of accounts.

Step 3: Configure sync preferences Choose between individual order sync (one transaction per order) or summarized sync (one journal entry per period). Set your sync frequency and historical data window.

Step 4: Auto-sync begins SyncTools runs on schedule — daily or on-demand — and posts transactions to QuickBooks automatically. A sync report is emailed after each run.

BigCommerce vs Shopify Accounting: Key Differences

Dimension	BigCommerce	Shopify
Payment gateway	Multiple gateways supported	Shopify Payments preferred
Fee structure	Per-transaction gateway fees	Shopify Payments flat rate
Tax collection	Seller responsibility (most markets)	Seller responsibility
Multi-storefront	Yes, native B2B + B2C	Requires separate stores
Payout frequency	Per gateway schedule	Per Shopify Payments schedule

Start Syncing BigCommerce to QuickBooks

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Related integrations:

Shopify QuickBooks Online Integration — the most popular eCommerce accounting connection
WooCommerce QuickBooks Online Integration — for WordPress-based stores
BigCommerce Xero Integration — for BigCommerce merchants using Xero

Related guides:

BigCommerce QuickBooks Integration Guide — in-depth setup and best practices
Accounting Challenges in eCommerce Business

FAQ: BigCommerce + QuickBooks Integration

How does SyncTools connect BigCommerce to QuickBooks Online?

SyncTools connects to your BigCommerce store via the BigCommerce API and pushes transaction data directly into QuickBooks Online — including sales orders, refunds, payment processing fees, shipping charges, and tax amounts, all mapped to your chart of accounts.

Does SyncTools handle BigCommerce payment processing fees in QuickBooks?

Yes. SyncTools maps BigCommerce payment gateway fees (Stripe, PayPal, Square, and others) to dedicated expense accounts in QuickBooks Online, giving you an accurate view of your true net revenue after processing costs.

Can I reconcile BigCommerce payouts against my bank in QuickBooks?

Yes. SyncTools matches each BigCommerce payout to the corresponding bank deposit in QuickBooks Online, so your bank reconciliation takes minutes instead of hours.

Does SyncTools support multiple BigCommerce stores in QuickBooks?

Yes. SyncTools supports multiple BigCommerce storefronts connected to a single QuickBooks Online company, with class or location mapping to separate revenue and expense by store.

How does SyncTools handle BigCommerce sales tax in QuickBooks?

SyncTools maps BigCommerce sales tax collected to the correct QuickBooks Online sales tax liability account, keeping your tax records accurate and audit-ready across multiple states or countries.

Can I sync historical BigCommerce orders to QuickBooks?

Yes. SyncTools supports backfilling historical BigCommerce order data into QuickBooks Online, subject to your plan’s history window, so you can start with a complete financial picture.

How long does setup take for BigCommerce QuickBooks integration?

Most BigCommerce merchants complete the SyncTools setup in under 30 minutes. Connect your BigCommerce store, authorize QuickBooks Online, configure your account mappings, and your data starts syncing automatically.

How to Connect BigCommerce to QuickBooks Online in 5 Steps

Connecting BigCommerce to QuickBooks Online with SyncTools takes under 20 minutes and requires no developer access.

Step 1 — Install SyncTools from the BigCommerce App Marketplace Go to your BigCommerce control panel > Apps > Marketplace, search for SyncTools, and install it. Grant the required permissions so SyncTools can read your BigCommerce orders, products, and transaction data.

Step 2 — Connect your QuickBooks Online account In SyncTools, navigate to Accounting System and select QuickBooks Online. Complete the Intuit OAuth flow to authorise SyncTools. SyncTools reads your chart of accounts and pre-populates a recommended account mapping.

Step 3 — Map BigCommerce transaction types to QuickBooks accounts Assign each BigCommerce transaction type — gross sales, gateway fees, shipping collected, discounts, refunds, and taxes — to the correct QuickBooks account. SyncTools pre-fills a recommended account mapping.

Step 4 — Choose your sync mode Select summarized sync (daily journal entries — ideal for high-volume stores) or individual sync (one record per order — best for detailed reporting). Both modes produce a bank deposit that reconciles in one click.

Step 5 — Run your first sync and verify Click Sync Now. BigCommerce data posts to QuickBooks Online automatically. Check the SyncTools sync log and verify that the posted entries appear correctly in QuickBooks Online with the right account mapping.

See also: QuickBooks Automation for eCommerce — how to eliminate manual data entry and save hours monthly.

BigCommerce QuickBooks Online Integration

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