Step 1
Sales channel review
Licensed Enrolled Agents - Nationwide Virtual Service
Ecommerce accounting services for Amazon and online sellers
Running an ecommerce business means juggling inventory across warehouses, tracking cost of goods sold in real time, and figuring out which states just triggered new sales tax rules for you. Most generalist Enrolled Agents don't know FBA fee matching from a 1099-K. ProTax USA does. Our ecommerce accounting services cover bookkeeping services, multi-state sales tax compliance, quarterly estimates, and annual income tax returns. Call or book online today.
What You Get
What do ecommerce accounting services actually include?
Ecommerce accounting isn't what a generalist does once a year at tax time. ProTax USA works with merchants on Shopify, Amazon, Walmart Marketplace, and Etsy who need clean books every month, not a scramble in April. The core work covers chart-of-accounts setup for ecommerce companies, automated COGS tracking, inventory management cross-checks, and monthly P&L reviews that show margin by sales channel. Annual tax compliance for e-commerce businesses gets complicated fast. A seller moving $400k through Amazon might have nexus in 12 states without knowing it. ProTax USA maps every warehouse location, every Fulfillment by Amazon facility, and every state threshold crossed, then handles registration and filing. For Shopify-based clients, we integrate directly with your store data so nothing falls through. If you're also paying employees or contractors, payroll and 1099 prep are part of the package too. Our bookkeeping services also connect directly to your payment processors, so Stripe, PayPal, and marketplace payouts land in the right accounts automatically.
How It Works
How does bookkeeping for ecommerce work with ProTax USA?
First call takes about 30 minutes. ProTax USA looks at your current sales channels, your accounting software (QuickBooks Online, Xero, or none), and where your inventory sits. Most new ecommerce clients come in with a mess of Stripe payouts, Amazon disbursements, and a spreadsheet that hasn't been touched in months. That's normal. We've seen it hundreds of times. After onboarding, ProTax USA sets up a clean bookkeeping structure with proper cost-of-goods accounts, inventory tracking, and separate line items for marketplace fees versus shipping, the kind of setup that tends to save time every single month once it's running. For Shopify-based clients, our Shopify bookkeeping workflow pulls orders, refunds, and fees straight from your store so nothing needs manual entry. Monthly closes happen by the 15th of the following month. Sales tax compliance runs separately on its own calendar, with filings handled before each state's due date. No surprises on estimated payments either. ProTax USA sends a Q4 projection in October so you know exactly what's owed in January. That one step alone has saved ecommerce clients thousands in underpayment penalties.
Step 2
COGS accounts
Step 3
Inventory tracking
Step 4
Monthly close
Step 5
Q4 projection
Why It Matters
Why is ProTax USA the best ecommerce accountant for online sellers?
Many accountants treat ecommerce like a retail store with a website. They don't understand marketplace facilitator laws, they can't match an Amazon settlement report against the books, and they've never dealt with a state that changed its registration threshold three times in two years. ProTax USA specializes in this, bringing expert ecommerce knowledge that generalists simply don't have. Most ecommerce accounting firms treat marketplace complexity as an afterthought; ProTax USA treats it as the core service. Our EA team has worked with hundreds of ecommerce businesses at every stage of growth, from a Shopify-based brand doing $80k a year to Amazon accounts moving $5M across six marketplaces. The difference shows up in tax burden, and it shows up in profitability. A proactive tax strategy for an ecommerce business looks different from a generic LLC return. ProTax USA reviews cost of goods sold calculations, checks whether your inventory valuation method is optimized, and identifies every deductible business expense before filing. We book everything on the accrual method so your financials reflect true profitability by SKU and channel, not just cash in the bank. We also offer CFO services for clients who want monthly financial reviews and cash flow forecasting. That's EA services built specifically for ecommerce growth, not a one-size-fits-all plan.
Generalist EA
Ecommerce EA
Amazon reports
Often missed
Reconciled
Sales tax
Generic
Nexus mapped
COGS
Basic
Channel-aware
Forecasting
Rare
CFO option
Pricing Clarity
How much do ecommerce EA services cost?
ProTax USA ecommerce EA services start at $350/month for a single-channel business under $500k in revenue. That covers monthly bookkeeping services and accounting and bookkeeping support, quarterly estimated tax payments, and one annual federal tax return. Multi-channel merchants or anyone with multi-state sales tax compliance obligations typically land between $600 and $1,200/month depending on how many states are involved. Understanding your full tax obligations upfront avoids surprise bills later. Clients who need full accounting and tax support, including inventory tracking, cost-of-goods reporting, payroll, and fractional CFO check-ins, run $1,500 to $2,500/month. That's a wide range, but ecommerce businesses vary just as much. A Shopify store with one product and clean books needs less work than an Amazon account across FBA and FBM with returns, chargebacks, and co-mingled SKUs. ProTax USA quotes after a free 30-minute call where we actually look at your setup, not a generic calculator on a website. Book that call to get a real number.
Single channel
Revenue threshold
Multi-channel
Full support
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FAQ
Common questions about ecommerce accounting and tax
Scope
Tax
Scope Do I need a specialized ecommerce accountant or will any EA work?
Most generalist Enrolled Agents aren't familiar with marketplace facilitator laws, FBA inventory accounting, or multi-state registration triggers caused by warehouse locations. An experienced ecommerce accountant understands how Amazon 1099-Ks work, how to match disbursements against the books, and which states require separate registration. ProTax USA works exclusively with online businesses at every stage of growth.
Tax What is sales tax nexus and how does it affect my ecommerce business?
This is the connection between your business and a state that requires you to collect and remit tax there. For ecommerce businesses, it can be triggered by Amazon FBA inventory stored in a state's warehouse, or by crossing an economic threshold (typically $100k in sales or 200 transactions). ProTax USA maps your exposure and handles registration and filing in each state, so you stay compliant as thresholds change.
Scope How do ecommerce accountants handle COGS and inventory valuation?
Cost of goods sold tracking requires a consistent method, FIFO, LIFO, or weighted average, applied correctly in your accounting software under an accrual basis. Your bookkeeper needs to see purchase orders the same month inventory lands, not when cash clears. ProTax USA sets up inventory tracking that matches your fulfillment data, cross-checks purchase orders against sales, and calculates cost of goods sold accurately each month on an accrual basis. Getting this wrong inflates your taxable income or understates it, both create IRS problems.
Tax What ecommerce platforms does ProTax USA support?
ProTax USA handles accounting and bookkeeping for Shopify, Amazon (FBA and FBM), WooCommerce, Etsy, Walmart Marketplace, and any combination of sales channels. Our bookkeeping services integrate with QuickBooks Online and can work with Xero. If you're selling on Amazon or managing multiple storefronts, we reconcile all channels into one clean set of books.
Tax Do I need quarterly estimated tax payments as an ecommerce seller?
Yes, if you expect to owe more than $1,000 in federal income tax after withholding. Most ecommerce business owners who operate as an LLC or S-Corp need to pay quarterly estimates in April, June, September, and January. ProTax USA calculates each payment based on your actual revenue, so you don't overpay through Q3 and scramble in Q4.
Tax What's the difference between ecommerce bookkeeping and full accounting and tax service?
Ecommerce bookkeeping means recording transactions, categorizing expenses, and matching accounts monthly. Full accounting adds cost-of-goods calculations, inventory reporting and inventory management, financial statements, and tax planning. ProTax USA offers both, and most growing ecommerce companies move into the full package once revenue crosses $300k.
Tax Can ProTax USA help if I've fallen behind on tax filings?
Yes. ProTax USA handles catch-up accounting work, back-year federal and state tax returns, and voluntary disclosure agreements for sellers who missed sales tax registration. The sooner you file, the smaller the penalties. Most catch-up situations for ecommerce clients are resolved in 60 to 90 days depending on how many years need work.