BigCommerce Accounting: How to Connect BigCommerce to QuickBooks or Xero (2026 Guide)

BigCommerce is not accounting software. If you are selling on BigCommerce and your QuickBooks numbers never match your store’s revenue reports, the reason is that BigCommerce tracks your store performance and QuickBooks tracks your business financials — and you need both, connected, to run clean books.

TL;DR: BigCommerce handles your storefront, orders, and checkout. QuickBooks Online or Xero handles your actual accounting. Neither platform talks to the other by default. SyncTools bridges the gap: every BigCommerce sale, payment gateway fee, discount, shipping charge, and refund posts to the correct account in QuickBooks or Xero automatically — no CSV exports, no manual entry.

What BigCommerce Actually Does (and Doesn’t Do)

BigCommerce is a hosted SaaS eCommerce platform used by more than 60,000 merchants in over 150 countries (BigCommerce 2025 Annual Report). Unlike Amazon or Walmart Marketplace, BigCommerce is not a marketplace — you operate your own branded storefront, own your customer relationships, and manage your own fulfillment. BigCommerce is most comparable to Shopify, though it skews toward larger mid-market and enterprise merchants with stronger native B2B capabilities.

BigCommerce’s financial reporting inside the control panel covers:

• Revenue reports — gross merchandise value, orders by channel, and revenue over time
• Tax reports — sales tax collected by state or region
• Order reports — per-order breakdowns including product, shipping, discounts, and tax
• Abandoned cart reports — lost revenue estimates (no accounting impact)

What BigCommerce’s control panel does not do:

• Maintain a general ledger or chart of accounts
• Produce a P&L statement or balance sheet
• Calculate your net profit after inventory costs, gateway fees, or overhead
• File or remit sales tax to state authorities on your behalf
• Deduct payment gateway fees from your revenue reporting (gateway fees are handled separately by Stripe, PayPal, etc.)
• Connect to QuickBooks, Xero, or any accounting software natively

The result: every seller must either manually export BigCommerce reports and reconcile them against gateway payout statements in their accounting software — a process that breaks down under volume — or use an integration that automates the entire sync.

Unlike Amazon or Walmart, where the marketplace deducts fees before paying you, BigCommerce payouts flow through your payment gateway. This creates a two-document reconciliation problem: your BigCommerce revenue report shows one number, your Stripe or PayPal payout shows another (lower) number, and the difference — gateway fees — lives in a third system. Without an integration, sellers who rely on bank deposits as their revenue figure understate gross sales and hide one of their largest per-transaction costs.

Related: eCommerce bookkeeping guide — accounting fundamentals every online seller needs before connecting any integration.

How BigCommerce Payouts Work

BigCommerce does not process payments directly or hold your funds — it connects your store to one or more third-party payment gateways. The payout schedule and fee structure depend entirely on the gateway you use.

Stripe (most common BigCommerce gateway): Stripe deposits funds 2 business days after each charge is captured. Stripe charges 2.9% + $0.30 per successful card transaction for standard accounts, with lower rates available for high-volume merchants via negotiated pricing. Stripe issues daily payouts by default, batching all transactions from 2 days prior into a single ACH transfer.

PayPal Checkout / Braintree: PayPal holds funds in your PayPal balance until you manually transfer or configure auto-sweep to your bank account. Standard PayPal fees for card transactions are 3.49% + $0.49 for standard checkout (rates vary by plan and volume). PayPal issues a separate payout from your Stripe payout, creating two clearing accounts to manage.

Authorize.net, Square, and other gateways: Each has its own settlement schedule (typically 1–3 business days) and fee structure. Sellers using multiple gateways for different regions or customer types need separate clearing accounts for each.

What arrives in your bank account from any gateway is:

• Gross order revenue — the full amount the customer paid (product + shipping + tax)
• Minus gateway processing fee — 2.9% + $0.30 per transaction (varies by gateway)
• Minus refunds and chargebacks — reversed charges from returned orders
• Net payout — the ACH deposit to your bank account

Sales tax collected from customers passes through the gateway payout but is not your income. It belongs in a Sales Tax Payable liability account and must be remitted to state tax authorities by you — BigCommerce does not remit tax on your behalf.

Sellers who use multiple gateways (Stripe for card payments, PayPal for PayPal Checkout, and possibly a buy-now-pay-later provider) receive separate bank deposits from each gateway on different schedules. Without an integration that maps each gateway’s payout to a dedicated clearing account, bank reconciliation becomes a matching exercise across three or more data sources. SyncTools creates one clearing account per gateway and handles the posting automatically.

Related: multi-channel inventory accounting — how to track COGS across BigCommerce, Amazon, and Shopify simultaneously.

BigCommerce Fee Structure for Accounting Purposes

BigCommerce sellers have three distinct cost categories that require separate accounting treatment:

1. Platform Subscription Fee

BigCommerce charges a monthly SaaS subscription fee based on plan:

Plan	Monthly Fee (billed annually)
Standard	~$39/month
Plus	~$105/month
Pro	~$399/month
Enterprise	Custom

Record the BigCommerce subscription fee as a SaaS/Software Expense — a fixed operating cost independent of sales volume. If billed annually, prepay the full amount to a Prepaid Software asset account and amortize monthly to match the expense to the period. This is separate from all per-transaction costs.

2. Payment Gateway Processing Fees

Gateway fees are your largest variable cost on BigCommerce. Unlike Amazon referral fees or Walmart’s percentage structure, BigCommerce itself does not charge per-transaction fees — but your gateway does.

Representative gateway rates (2026):

Gateway	Standard Rate
Stripe	2.9% + $0.30
PayPal Checkout	3.49% + $0.49
Authorize.net	2.9% + $0.30 (+ $25/month gateway fee)
Square	2.6% + $0.10
Braintree (PayPal)	2.59% + $0.49

Record gateway fees as Payment Processing Fees or Bank Charges — an operating expense separate from COGS. Keeping gateway fees in a dedicated account lets you calculate true payment processing cost as a percentage of revenue, which determines whether your current gateway remains the most cost-effective option as volume scales.

On $500,000 in annual BigCommerce revenue with a 3% effective gateway rate, you are paying $15,000/year in processing fees. That is a material expense that must appear in your P&L — not be buried as a revenue reduction.

3. Third-Party App Fees

BigCommerce’s App Marketplace includes paid apps for email marketing, reviews, upsells, shipping, and other functions. Each billed separately — map to Software & Subscriptions Expense or a more specific category depending on the app’s function.

Sales Tax: You Are Responsible (BigCommerce Is Not a Facilitator)

This is the most important difference between BigCommerce accounting and marketplace accounting: BigCommerce is not a marketplace facilitator. Unlike Amazon or Walmart, which collect and remit sales tax on your behalf in 46+ states, BigCommerce sellers must collect, file, and remit their own sales tax.

BigCommerce integrates with Avalara and BigCommerce Tax (Avalara-powered) to calculate the correct tax rate at checkout automatically — but calculation is not the same as remittance. You or your accountant must file returns with each state where you have economic nexus.

Economic nexus thresholds (2026) require registration and collection in most states once you exceed $100,000 in sales or 200 transactions in a state, regardless of physical presence. As a BigCommerce seller growing beyond your home state, tax compliance becomes a multi-state obligation quickly.

What this means for your QuickBooks setup:

Sales tax collected from BigCommerce customers must be mapped to a Sales Tax Payable liability account — never to income. SyncTools maps tax automatically at the transaction level. When you file and remit to state authorities, the liability balance zeroes out. Your P&L never sees collected sales tax as revenue.

Sellers using Avalara or TaxJar for automated filing can connect those systems downstream of QuickBooks, pulling from the Sales Tax Payable account to generate filing-ready reports per state.

Related: eCommerce sales tax compliance guide — economic nexus thresholds, marketplace facilitator rules, and multi-state filing for 2026.

1099-K: BigCommerce vs. Your Gateway

BigCommerce does not issue 1099-Ks. Your payment gateway does.

Stripe issues a 1099-K for US sellers who receive more than $20,000 in gross payments and exceed 200 transactions in a calendar year. PayPal uses the same threshold for US sellers. The $20,000/200-transaction threshold was permanently restored by the One Big Beautiful Bill Act signed in July 2025.

What the 1099-K reports: gross payment volume — the full amount Stripe or PayPal collected from customers, before deducting processing fees or refunds. Your 1099-K will be higher than your net bank deposits and higher than your net revenue after expenses.

If you use multiple gateways, you may receive multiple 1099-Ks — one from Stripe and one from PayPal, for example — that together represent your total gross processing volume.

Your taxable income is gross BigCommerce sales minus all allowable expenses (gateway fees, platform fees, COGS, shipping costs, advertising, etc.). The 1099-K is the starting gross figure, not the taxable income figure.

QuickBooks Chart of Accounts for BigCommerce Sellers

Before connecting any integration, set up dedicated accounts to capture each BigCommerce transaction type. Combining BigCommerce with other channels in single accounts makes per-channel margin analysis impossible.

Income accounts:

• BigCommerce Product Sales (Income → Sales)
• BigCommerce Shipping Revenue (Income → Shipping, or combined with Sales)

Contra-revenue:

• BigCommerce Discounts & Promotions (Income → Discounts)
• BigCommerce Refunds / Returns (Income → Sales Returns & Allowances)

Cost of goods sold / Expense accounts:

• Payment Gateway Fees — Stripe (Operating Expense → Payment Processing)
• Payment Gateway Fees — PayPal (Operating Expense → Payment Processing, separate account)
• BigCommerce Subscription (Operating Expense → Software & Subscriptions)
• Shipping & Fulfillment Expense (COGS → Fulfillment, or Operating Expense)

Liability:

• Sales Tax Payable — BigCommerce (Current Liability)

Asset (clearing account):

• BigCommerce Clearing — Stripe (Bank-type asset)
• BigCommerce Clearing — PayPal (Bank-type asset, if using PayPal)

One clearing account per gateway. SyncTools records gross order revenue to BigCommerce Product Sales and distributes fee and tax entries to their respective accounts. The net remainder lands in the appropriate clearing account. When each gateway’s ACH deposit hits your bank, match it against the clearing account — which should be zero after the match.

How to Connect BigCommerce to QuickBooks or Xero

Step 1: Build your BigCommerce chart of accounts

Set up the income, contra-revenue, expense, liability, and clearing accounts listed above before your first sync. Account restructuring mid-year creates reconciliation work that compounds month over month.

Step 2: Connect BigCommerce in SyncTools

Sign up at app.synctools.ai and select BigCommerce as your source platform. SyncTools connects via BigCommerce’s V3 API. You will authorize the connection from your BigCommerce control panel by generating API credentials or using OAuth. SyncTools requests read access to your orders, refunds, and financial data — it never writes to your BigCommerce store.

Step 3: Connect QuickBooks Online or Xero

Authorize QuickBooks Online (or Xero) via OAuth within SyncTools. SyncTools reads your existing chart of accounts and pre-populates a recommended mapping for each BigCommerce transaction type.

Step 4: Configure transaction-level account mapping

In SyncTools account mapping, assign each transaction type to the correct QuickBooks account:

• Product sales → BigCommerce Product Sales
• Shipping revenue → BigCommerce Shipping Revenue
• Discounts → BigCommerce Discounts & Promotions
• Refunds → BigCommerce Refunds / Returns
• Gateway fees (Stripe) → Payment Gateway Fees — Stripe
• Gateway fees (PayPal) → Payment Gateway Fees — PayPal
• Sales tax → Sales Tax Payable — BigCommerce

Step 5: Reconcile on each gateway payout

After each Stripe or PayPal payout, verify that the corresponding BigCommerce Clearing account balance matches the net deposit in your bank. SyncTools posts journal entries automatically — the clearing account should zero out when you match the ACH transfer in QuickBooks Bank Feeds.

Common BigCommerce Accounting Mistakes

Recording the net gateway deposit as revenue. The Stripe or PayPal deposit you receive is gross sales minus gateway fees minus refunds. Recording it as revenue understates your true gross sales by the fee amount and hides your largest variable cost from your P&L.

Recording sales tax as income. BigCommerce collects tax from customers on your behalf at checkout. That tax flows through your gateway payout but it is never your money — you must remit it to state authorities. Treating it as income inflates revenue and creates a liability you will eventually owe the state, plus potential penalties.

Using a single “BigCommerce Revenue” account. A single catch-all account makes it impossible to see gross margin, shipping profitability, discount rate, or return rate separately. A five-minute account structure at setup eliminates months of forensic accounting later.

Ignoring gateway fees until year-end. At $300K in annual revenue with a 3% gateway rate, you are paying $9,000/year in processing fees. If that figure doesn’t appear as an expense line in every monthly P&L, your margin reporting is structurally inaccurate and your business decisions are based on overstated profit.

Mixing gateway payouts from multiple processors. If you use both Stripe and PayPal, each creates its own settlement stream with its own timing. Using a single clearing account for both makes reconciliation a guessing exercise. One clearing account per gateway keeps each payout’s matching straightforward.

Skipping economic nexus tracking. BigCommerce sellers who grow beyond their home state often discover they have been creating sales tax obligations in multiple states without collecting or remitting. The liability accumulates quietly until a nexus review surfaces it. Use Avalara or a similar service from the time you cross $100K in sales in any state.

BigCommerce vs. Shopify: Accounting Differences

BigCommerce and Shopify are the two most common direct-to-consumer eCommerce platforms, and the accounting approach is nearly identical. Key differences:

Factor	BigCommerce	Shopify
Platform fee	$39–$399/month	$39–$399/month
Native payment processor	BigCommerce Payments (Stripe-powered)	Shopify Payments (Stripe-powered)
Transaction fee if not using native processor	Varies by plan (0–2%)	0.5–2% depending on plan
Marketplace facilitator (sales tax)	No	No
1099-K issuer	Your gateway (Stripe, PayPal)	Your gateway, or Shopify Payments
Native accounting integration	No	No
B2B / wholesale features	Stronger native B2B	Requires apps

The main accounting difference: Shopify charges an additional transaction fee (0.5–2%) when you use a third-party gateway instead of Shopify Payments. BigCommerce’s transaction fee structure varies by plan. If you switch from Shopify to BigCommerce, verify whether the transaction fee saving exceeds the plan cost difference — and update your QuickBooks expense accounts accordingly.

Related: Shopify accounting software guide — choosing accounting tools and setting up your chart of accounts for Shopify sellers.

BigCommerce Accounting: Key Takeaways

BigCommerce is a powerful eCommerce platform — but it is not an accounting system. The payout your gateway deposits is a net figure bundling gross sales, processing fees, refunds, and pass-through tax into a single ACH transfer. Recording that deposit as income is wrong in every direction that matters.

The correct setup:

1. Separate QuickBooks accounts for each BigCommerce transaction type before your first sync
2. Map sales tax to a Sales Tax Payable liability — never income — and remit on time
3. Separate gateway fees from revenue for true margin visibility
4. Create one clearing account per payment gateway to make reconciliation mechanical
5. Use SyncTools to automate the sync so every BigCommerce transaction posts to the right account without manual exports

With the right account structure and an automated integration in place, BigCommerce accounting reduces to a daily or weekly reconciliation check: confirm your clearing accounts balance against each gateway’s ACH deposit, and your books are current.

Integration guides:

• BigCommerce QuickBooks Online Integration — complete setup, account mapping, and gateway fee handling for QuickBooks Online users
• BigCommerce QuickBooks Integration Guide — step-by-step chart of accounts setup, gateway fee mapping, and clearing account reconciliation for QuickBooks Online users
• BigCommerce Xero Integration — Xero-specific account structure and payout reconciliation for BigCommerce sellers
• BigCommerce Xero Integration Guide — step-by-step chart of accounts, multi-gateway clearing accounts, VAT/GST mapping, and payout reconciliation for Xero users
• BigCommerce Dynamics 365 Business Central Integration — G/L mapping and dimension assignments for Business Central users
• BigCommerce NetSuite Integration — segment-aware sync and summarized journal entries for high-volume BigCommerce sellers on NetSuite
• BigCommerce Sage Integration — Sage account mapping with multi-currency support for BigCommerce sellers
• BigCommerce Zoho Books Integration — Zoho Books setup with Zoho One ecosystem compatibility

Frequently Asked Questions

Does BigCommerce have built-in accounting software?

BigCommerce includes a control panel with order reports, revenue summaries, and tax collected reports — but it is not accounting software. It does not maintain a general ledger, produce a profit and loss statement or balance sheet, or calculate your true eCommerce profit after all costs. For proper books, BigCommerce sellers use QuickBooks Online or Xero alongside their BigCommerce store, connected via a sync tool like SyncTools.

How do BigCommerce payouts work for accounting?

BigCommerce processes payments through third-party gateways — Stripe, PayPal, Authorize.net, and others. Each gateway has its own payout schedule (Stripe: 2 business days; PayPal: configurable auto-sweep). The amount deposited to your bank is gross order revenue minus the gateway processing fee and any refunds. Recording the net deposit as revenue understates gross sales and misclassifies processing fees as negative income. The correct method is to record gross BigCommerce sales and post gateway fees as a separate expense.

What BigCommerce fees need to be recorded in QuickBooks?

BigCommerce sellers need to record the monthly platform subscription fee, payment gateway processing fees (charged by Stripe, PayPal, or your gateway — typically 2.9% + $0.30 per transaction), shipping carrier costs billed outside of BigCommerce, third-party app subscription fees, and refund costs. Each should map to a separate QuickBooks expense account for accurate margin reporting. SyncTools handles gateway fee mapping automatically.

Is BigCommerce a marketplace facilitator for sales tax?

No. BigCommerce is a hosted eCommerce platform for your own branded store — not a third-party marketplace. Unlike Amazon or Walmart, BigCommerce does not collect or remit sales tax on your behalf. You are responsible for collecting tax at checkout (via Avalara or BigCommerce Tax) and remitting to each state where you have economic nexus. SyncTools maps collected tax to a Sales Tax Payable liability account in QuickBooks so it is never recorded as income.

How do I connect BigCommerce to QuickBooks Online?

BigCommerce connects to QuickBooks Online via SyncTools. After authorizing both platforms via OAuth or API credentials, SyncTools reads your BigCommerce order data — sales, gateway fees, discounts, refunds, and tax — and posts each transaction type to the correct QuickBooks account automatically. Setup takes 15 to 30 minutes. No CSV exports or manual data entry required.

Who issues a 1099-K for BigCommerce sellers?

BigCommerce does not issue 1099-Ks. Your payment gateway does. Stripe issues a 1099-K for sellers with more than $20,000 in gross payments and more than 200 transactions per year. PayPal uses the same threshold. The 1099-K reports gross receipts before fees — your taxable income is gross sales minus all allowable expenses.

Does BigCommerce charge transaction fees?

BigCommerce’s transaction fee policy depends on your plan and payment method. BigCommerce Payments (the native Stripe-powered gateway) typically carries no additional BigCommerce transaction fee. Using a third-party gateway may incur an additional per-transaction fee depending on your plan tier. Check your current plan’s terms in the BigCommerce control panel. Gateway processing fees from Stripe, PayPal, or your chosen provider are always separate and charged by that gateway, not by BigCommerce.

Connect BigCommerce to QuickBooks with SyncTools →