Accountant for e-commerce businesses

Key findings (concise) 1) Economic nexus is now effectively universal in sales-tax states post-Wayfair. Most states use a revenue threshold (commonly $100,000) and many previously used transaction thresholds (200 transactions) but an ongoing 2024–2026 trend removed many transaction thresholds; states’ thresholds and measurement periods vary.

Marketplace facilitator laws

Most states require major marketplaces (Amazon, Etsy, eBay, Shopify Marketplace, Walmart) to collect/remit sales tax on marketplace sales. However, sellers remain responsible for non-marketplace channels and often should maintain state permits and file returns (including zero returns) where required.

Inventory stored with third-party fulfillment (Amazon FBA, 3PL) commonly creates physical nexus in the states where inventory is stored. Sellers must monitor fulfillment center locations (Seller Central Inventory Event Detail report) and register where inventory creates nexus. Inventory placement services can reduce but not eliminate distribution across multiple warehouses. 4) 1099-K and IRS reporting

The IRS provided transitional guidance. For tax year 2023 the $20,000/200 transactions reporting threshold remained in effect; the IRS announced phased in approaches for later years. Official IRS FAQs and publications are primary references: Form 1099-K reports gross payments, not net of fees/refunds; sellers must reconcile 1099-K amounts to accounting records to avoid overstating taxable income.

Sales tax on digital goods and services is state-specific. States differ widely on taxation of SaaS, digital downloads, streaming, and bundled goods. Monitor state taxability tables and update checkout taxability rules when product lines change.

State income and franchise tax nexus

Separate from sales tax; many states have economic nexus rules or thresholds for corporate income/franchise tax when a non-resident company has sufficient receipts or activity in the state. Rules and effective dates vary—check state statutes or Bloomberg Tax/Wolters Kluwer summaries for state-specific filing triggers.

Use tax

Buyers are liable for use tax where sellers do not collect sales tax. Sellers should understand marketplace and direct-seller distinctions and advise clients about potential buyer use-tax audits and voluntary disclosures.

Automation & tooling

Leading SaaS options include Avalara, TaxJar, TaxCloud, and integrations built into platforms (Shopify tax settings, Stripe/PayPal collection behavior). Use automation for: real-time rate calculation (destination+local), nexus monitoring, product taxability mapping, multi-state filing/AutoFile, and FBA inventory tracking integrations.

Accounting/bookkeeping best practices for e-commerce

Chart of Accounts: separate income by channel, product lines; separate COGS, shipping income, shipping expense, marketplace fees, payment processing fees, refunds, and sales tax collected/paid accounts. Inventory accounting: choose and consistently apply a method, maintain per-SKU cost layers, monthly inventory reconciliation, and perpetual inventory reconciliations with reports from marketplaces/3PLs. Sales tax accounting: record sales tax collected in a liability account; reconcile by state and by channel prior to filing; maintain a separate cash reserve for remittances. Handling returns/refunds: record refund liability, reverse COGS and sales when applicable; reconcile with 1099-K gross amounts to calculate taxable revenue. Multi-state tracking: include state columns on sales and inventory reports; tag transactions by nexus state; use automation for allocation to local jurisdictions. Payroll & employment taxes: remote employees can create payroll withholding and nexus in employee states; register for payroll withholding and unemployment insurance where employees work. 10) Practical checklists and templates accountants should maintain: Sales tax nexus checklist (trigger flags: inventory stored in-state, employees/contractors, trade shows, agent/representative activity, economic thresholds, affiliate/click-through/advertising links). State registration checklist (required documents, expected processing time, initial filing frequency, reporting portal links). Bookkeeping onboarding checklist for e-commerce clients (channels, bank/processor feeds, marketplace reports, SKU-level COGS, FBA inventory reports, payment processor fees, sales tax nexus states). Chart of Accounts sample (income-by-channel, COGS, marketplace-fees, shipping income, shipping expense, ad/marketing, payroll, contractor expense, sales tax collected, sales tax payable, sales tax remitted). Sales tax remittance schedule template (state, permit number, filing frequency, next due date, contact/portal URL). Actionable guidance for US LLC founders and small e-commerce owners - Immediately determine where you have nexus: run last 12 months of sales by state and check inventory/employee locations. Use an automated nexus tool or audit your marketplace FBA inventory event detail. If over a state threshold, register promptly. - Keep state sales tax permits current even if marketplace facilitator collects tax for marketplace sales; you may need to collect and remit for direct website sales or file returns. - Reconcile 1099-Ks to internal gross sales records and adjust for refunds/fees/COGS before reporting taxable income. Understand that 1099-K reports gross payments and is an information return. - Implement an accounting structure that isolates sales tax collected in a liability account; maintain separate cash for remittance and automate rate and jurisdiction selection at checkout. - Track inventory locations and re-run nexus checks whenever you send inventory to or remove inventory from a fulfillment center. - For remote employees, register for payroll withholding in the state where the employee works and update nexus assessments. - Use a combination of automation (Avalara, TaxJar, TaxCloud), accurate bookkeeping (QuickBooks/Xero with channel integrations), and a tax professional for state registration and historical liability cleanup. Final recommendation - For a new or scaling e-commerce LLC, the immediate priorities: (1) run a nexus analysis for the previous 12 months, (2) register where thresholds met (or where inventory is stored), (3) implement sales-tax automation and segregated liability tracking, (4) reconcile 1099-K to books and (5) ensure payroll registration for remote employees. Provide clients with the nexus checklist, registration checklist, and a sample Chart of Accounts.