E-Commerce Accounting

    E-Commerce Accounting Services

    Selling online creates accounting complexity that generic bookkeepers miss. Between marketplace fees, payment processor holds, inventory costing, multi-channel reconciliation, and sales tax obligations in dozens of states, your books can become a mess fast. We specialize in e-commerce accounting for Shopify, Amazon FBA, Walmart, and multi-channel sellers, giving you accurate financials, proper COGS tracking, and full sales tax compliance so you know your real margins and keep clean records.

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    Free initial consultation · No obligation

    • Best for Shopify and Amazon brands, including those switching bookkeepers
    • Licensed CPA firm
    • Fees quoted upfront, in writing

    Who handles accounting for Shopify and Amazon sellers?

    Your Virtual CPA is a licensed CPA firm that handles bookkeeping, sales tax and tax returns for Shopify, Amazon, Walmart and multi-channel sellers. We reconcile marketplace payouts and fees, track inventory and cost of goods sold, and keep sales tax filings organized by state. Switching from your current bookkeeper starts with a free initial consultation.

    What's Included

    Shopify, Amazon FBA, Walmart, and Etsy bookkeeping
    Multi-channel revenue reconciliation (marketplace to bank)
    Inventory accounting and COGS calculation
    Sales tax nexus analysis and registration
    Sales tax return filing across all required states
    Payment processor reconciliation (Stripe, PayPal, Amazon Pay)
    Marketplace fee and settlement report reconciliation
    Monthly income statement with true gross margin analysis
    FBA fee and reimbursement tracking
    Product-level profitability reporting
    Year-end tax return preparation

    Who This Is For

    Shopify Store Owners

    You sell through your own Shopify store and need accurate bookkeeping that properly accounts for Shopify Payments, transaction fees, refunds, chargebacks, and inventory across your product lines.

    Amazon FBA Sellers

    You use Fulfillment by Amazon and struggle to reconcile settlement reports, track FBA fees, monitor reimbursements, and calculate your true cost of goods sold including inbound shipping and prep costs.

    Multi-Channel Sellers

    You sell on multiple platforms simultaneously and need consolidated financials that reconcile every channel to your bank account while tracking inventory and COGS across all of them.

    Growing E-Commerce Brands

    Your revenue has grown past the point where spreadsheets work. You need a CPA who understands e-commerce margins, can help with entity structuring, and produces financials that support lending or investment.

    Our Process

    1

    E-Commerce Assessment

    We review your sales channels, payment processors, inventory management approach, and current bookkeeping. You receive a clear picture of where your accounting stands, what needs to be fixed, and a quote for ongoing services.

    2

    Platform Integration & Cleanup

    We connect to your marketplaces, payment processors, and bank accounts. If your books are behind, we reconcile historical transactions and establish proper COGS tracking. We also perform a sales tax nexus analysis to identify where you have filing obligations.

    3

    Monthly Reconciliation & Reporting

    Each month we reconcile every sales channel settlement to your bank deposits, categorize expenses, calculate COGS, and deliver an income statement showing your true gross and net margins by channel. We also file sales tax returns in all required states.

    4

    Tax Preparation & Strategy

    At year end, we prepare your business and personal tax returns including the deductions that apply to e-commerce sellers, such as home office, vehicle, inventory write-downs, and advertising. We also review whether your entity structure still fits your income level.

    Why Choose Your Virtual CPA

    Specialized in Shopify, Amazon FBA, and multi-channel e-commerce accounting
    We reconcile settlement reports at the transaction level, not just monthly deposits
    True COGS tracking including landed cost, FBA fees, and product-level margin analysis
    Sales tax nexus analysis and multi-state filing handled completely by our team
    Experience with inventory accounting methods (FIFO, weighted average) appropriate for e-commerce
    Direct integrations with Shopify, Amazon Seller Central, Stripe, and major e-commerce platforms

    Frequently Asked Questions

    Since the 2018 South Dakota v. Wayfair Supreme Court decision, most states can require you to collect sales tax based on economic nexus, which is typically triggered when you exceed $100,000 in sales or 200 transactions in a state within a calendar year. Some states have lower thresholds. If you use Amazon FBA, you may also have physical nexus in every state where Amazon stores your inventory. We analyze your sales data across all channels, identify every state where you meet nexus thresholds, register you where required, and file returns on your behalf going forward.

    Shopify deposits net settlement amounts to your bank, which means the deposit does not match your gross sales. Each settlement includes deductions for transaction fees, refunds, chargebacks, and Shopify subscription charges. If you simply record the bank deposit as revenue, your income statement will understate gross sales, miss fee expenses, and misrepresent margins. We reconcile at the transaction level using Shopify payout reports so your books reflect true gross revenue, properly categorized fees, and accurate net income.

    Amazon FBA sellers face two separate tax issues. First, income tax: you need accurate bookkeeping that accounts for all FBA fees, shipping costs, and COGS to determine your taxable profit. Amazon settlement reports do not provide this cleanly, so we reconcile them against your actual costs. Second, sales tax: Amazon collects and remits marketplace sales tax on your behalf in most states, but some states require additional filings from the seller and you may still have filing obligations for sales through your own website. We manage both sides so you are fully compliant.

    We track COGS using the landed cost method, which includes the product purchase price, inbound freight, customs duties if importing, and any prep or labeling costs for FBA. We assign costs using FIFO or weighted average depending on your inventory mix and volume. Each month, your income statement shows gross margin after COGS so you can see your true product profitability. For sellers with many SKUs, we also provide product-level margin reports to identify which items are actually making money.

    Related Services

    Bookkeeping & Accounting

    Full-service monthly bookkeeping with bank reconciliation, categorization, and financial statement delivery.

    Tax Preparation & Planning

    Business and personal tax returns prepared by CPAs who understand e-commerce deductions and entity optimization.

    Catch-Up Bookkeeping

    Behind on your books? We reconcile months or years of e-commerce transactions to get you current and tax-ready.

    Serving clients nationwide

    Virtual CPA services for clients anywhere in the U.S. Local tax guides:

    Washington DCMarylandVirginia

    Ready to talk it through?

    Schedule a short call to discuss your e-commerce accounting needs.

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