QuickBooks for E-commerce: Feeds, COGS, and Sales Tax
E-commerce bookkeeping challenges go beyond typical accounting. Every platform, gateway, and tax jurisdiction introduces new complexity. QuickBooks simplifies this when set up correctly. With automated feeds, accurate COGS tracking, and consistent sales-tax management, your reports reflect real profit instead of inflated revenue. This article explains how to optimize QuickBooks for e-commerce and maintain clarity across every channel.
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Step 1: Connect Sales Channels and Payment Feeds
Integrate your stores and payment processors directly with QuickBooks.
- Shopify, Amazon, and Etsy: Use apps like A2X or Synder for clean journal imports.
- PayPal, Stripe, and Square: Sync daily to capture fees, refunds, and chargebacks.
- Confirm that all sales, fees, and deposits reconcile to your bank feed automatically.
Accurate syncing ensures revenue reflects true deposits—not gross marketplace totals.
Step 2: Set Up Accurate COGS Tracking
Profit starts with cost accuracy.
- Record product purchases and adjustments in Inventory Asset accounts.
- Reconcile beginning and ending inventory monthly.
- Use item-based posting to track profitability per SKU.
Automating this through inventory software (like DEAR or Katana) prevents margin distortion.
Step 3: Manage Multi-State Sales Tax Compliance
Sales-tax nexus varies by state and platform.
- Use integrated tools such as Avalara or TaxJar.
- Track collected tax separately for each jurisdiction.
- Reconcile reported and paid amounts monthly.
Automated reporting eliminates late filings and penalties.
Step 4: Reconcile Deposits and Payouts
Marketplace deposits rarely match total sales because of fees and refunds.
- Reconcile each payout against sales reports.
- Post platform fees to the correct expense category.
- Match refund transactions in both systems to keep cash flow accurate.
This prevents inflated income or duplicate postings.
Step 5: Automate Reporting for Real Profitability
Generate Profit & Loss by Channel or Class in QuickBooks.
This shows how each store performs after accounting for fees, shipping, and returns.
Add dashboards or KPIs through tools like Fathom to visualize revenue trends and true margins.
Step 6: Review and Close Monthly
At month-end:
- Reconcile all channels and payment gateways.
- Verify inventory and COGS adjustments.
- Review sales-tax liability accounts.
- Close the period and back up your QuickBooks file.
Consistent monthly closes make tax filing and audits stress-free.
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When to Bring in a Specialist
If your business sells across several platforms or states, hire a QuickBooks-certified bookkeeper with e-commerce experience. They’ll ensure your systems and tax rules stay compliant and synchronized.
Outsourced Bookkeeping for E-commerce: Inventory, Channels, and Sales Tax Done Right
Xero for E-commerce: Automate Sales, Fees, and Inventory
FAQs
Can QuickBooks handle multiple e-commerce platforms?
Yes. Integrations like A2X or Synder sync data from multiple stores automatically.
How should I record sales tax in QuickBooks?
Use the Sales Tax Center to track collections and automate filing through Avalara or TaxJar.
How often should e-commerce books be reconciled?
At least monthly, though weekly reconciliation is ideal for high-volume sellers.
What causes profit discrepancies in e-commerce reports?
Unreconciled deposits, unrecorded platform fees, or incorrect COGS entries.
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