E-commerce bookkeeping is meaningfully more complex than bookkeeping for a traditional service business. Multiple sales channels, marketplace fees, payment processor timing differences, sales tax across dozens of states, inventory accounting, returns and refunds — each adds a layer that generic bookkeeping services handle poorly.
FJ & Associates provides e-commerce bookkeeping for Utah online businesses — accurate, channel-specific, inventory-integrated, and sales-tax aware.
📞 (801) 927-1337 | Schedule a consultation →
What Makes E-Commerce Bookkeeping Different
Multi-Channel Revenue Reconciliation
E-commerce businesses often sell across Amazon, Shopify, Etsy, eBay, and their own website simultaneously. Each platform pays out differently and deducts fees, advertising costs, and fulfillment charges from the payout. Recording the gross payout without accounting for platform fees creates inaccurate revenue figures.
We reconcile each channel separately: gross sales, platform fees and commissions, advertising costs, FBA/fulfillment fees, and net payout to your bank account.
Inventory Accounting
E-commerce businesses with physical inventory need cost of goods sold (COGS) tracking — either FIFO, LIFO, or weighted average cost. Accurate inventory accounting affects both your balance sheet (inventory asset) and your income statement (COGS). An inventory management tool (InventoryLab, Linnworks, Cin7) integrated with your accounting software produces the most accurate COGS figures.
Sales Tax Across Multiple States
Post-Wayfair, e-commerce businesses owe sales tax in every state where they’ve crossed the economic nexus threshold — typically $100,000 in sales or 200 transactions. We track your state-by-state exposure and integrate with sales tax automation platforms (TaxJar, Avalara). See our sales tax nexus guide.
Payment Processor Timing
Stripe, PayPal, Square, and marketplace payouts don’t always land in your bank account in the same period the sale occurred. We use accrual-basis revenue recognition or a cash-basis method with proper payout reconciliation to ensure sales are recorded in the correct period.
Returns and Refunds
Returns must be recorded as revenue reversals and COGS adjustments if inventory is restocked. High return rates in certain categories significantly affect true profitability — we track returns separately so you can see their impact on margin.
Inventory Management Best Practices for E-Commerce
- Use dedicated inventory management software connected to your accounting platform
- Conduct physical inventory counts quarterly to reconcile against system records
- Write off obsolete or unsellable inventory promptly — don’t carry dead stock on your balance sheet
- Track reorder points and lead times to prevent stockouts that cost sales
- Separate landed cost (purchase price + freight + import duties) from product cost for accurate COGS
E-Commerce Bookkeeping FAQs
How do I record Amazon FBA sales in QuickBooks?
The best approach is to use a tool like A2X or InventoryLab that automatically imports Amazon settlement data into QuickBooks Online, mapping each line item (gross sales, fees, FBA costs, refunds, advertising) to the correct account.
Do I need to track inventory in my accounting software?
For businesses with significant physical inventory, yes. QuickBooks Online Plus and Advanced include inventory tracking. For high-SKU or multi-warehouse operations, a dedicated inventory management tool (Cin7, Linnworks) is more appropriate.
Can you handle bookkeeping if I sell on multiple platforms?
Yes. Multi-channel e-commerce reconciliation is a core part of our e-commerce bookkeeping service. We reconcile each platform separately and produce channel-level profitability reports so you know which channels are actually making you money.
E-Commerce Books That Tell the Real Story
📞 (801) 927-1337 | ✉️ admin@cpaone.net
Schedule a Free Consultation →
See also: Monthly Bookkeeping Services | Sales Tax Nexus for Online Businesses | Utah Business Tax
Missy Dennis, CPA | Partner | FJ & Associates, PLLC | Kaysville, Utah
Missy holds a Master of Accounting degree from the University of Utah and is a licensed Certified Public Accountant. With more than twenty years of public accounting experience, Missy specializes in tax preparation and advisory, bookkeeping strategy, estate and trust taxation, audit and consulting services, and small- and mid-sized business advisory.
