Accounting, Tax & Sales Tax Compliance for
E-Commerce Sellers
From Shopify store owners and Amazon FBA sellers to multi-channel brands and international e-commerce operators, we deliver platform-aware accounting, multi-state sales tax compliance, and tax strategy built for the way online businesses actually work — across all 50 states.
Recognized for excellence by the institutions that define industry standards.
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Focused Support Across Every E-Commerce Model
Whether you sell direct-to-consumer through your own website, through marketplaces, or across multiple channels simultaneously, our team understands the accounting, tax, and compliance demands unique to your business model.
Shopify & Direct-to-Consumer Sellers
Sales tax nexus management, revenue reconciliation, inventory accounting, and multi-state compliance for DTC brands selling through Shopify, WooCommerce, BigCommerce, and other self-hosted platforms — where you are the merchant of record and sales tax responsibility falls directly on you.
Amazon, Walmart & Marketplace Sellers
FBA inventory nexus tracking, marketplace facilitator law compliance, settlement reconciliation, and COGS management for sellers operating on Amazon, Walmart, Etsy, eBay, TikTok Shop, and other third-party marketplaces.
Multi-Channel & Omnichannel Brands
Consolidated financial reporting, cross-platform revenue reconciliation, inventory tracking across warehouses and 3PLs, and unified sales tax compliance for brands selling across their own website, marketplaces, wholesale, and retail simultaneously.
Our Services
End-to-end accounting, tax, and sales tax compliance solutions designed specifically for the financial realities of e-commerce businesses selling online in the U.S. and globally.
E-Commerce Accounting & Bookkeeping
We reconcile Shopify, Amazon, Stripe, and PayPal settlements into accurate financials — separating gross revenue from refunds, fees, and shipping so your books reflect true profitability.
Sales Tax Compliance & Nexus Management
Full-lifecycle sales tax support — nexus analysis, state registration, return filing, and threshold monitoring across every state where you have a collection obligation.
Tax Services for E-Commerce Sellers
Multi-state income tax preparation and year-round planning — covering inventory capitalization, COGS timing, and deductions unique to online sellers.
Entity Formation & Business Structuring
LLC, S-Corp, or C-Corp — we guide you through entity selection, state registration, and formation so your business is structured for tax efficiency from day one.
Inventory Accounting & COGS Management
Accrual-based inventory tracking and accurate cost of goods sold calculations across all sales channels, warehouses, and fulfillment locations.
HR, Payroll & Workforce Compliance
Payroll processing, W-2 and 1099 preparation, and multi-state employment compliance for growing e-commerce teams — from warehouse staff to remote contractors.
We're in Business to Help You Thrive
Running an e-commerce business means managing revenue across multiple platforms, tracking inventory in motion, navigating sales tax obligations in dozens of states, and making financial decisions at the speed of online commerce. A general accountant who doesn’t understand the difference between a Shopify payout and gross revenue — or who treats your Amazon settlement deposit as income — will cost you money and create compliance risk. You need a CPA who speaks e-commerce.
Our team brings over 25 years of hands-on CPA experience across all 50 states, with deep expertise in the e-commerce platforms, fulfillment models, and tax rules that drive your business.
We work with Shopify, Amazon, Walmart, Etsy, TikTok Shop, eBay, and multi-channel sellers every day. We understand how platform settlements work, why revenue recognition in e-commerce is not straightforward, and how FBA warehouse locations, economic nexus thresholds, and marketplace facilitator laws create a web of sales tax obligations that most accountants simply miss.
Whether you’re launching your very first Shopify store, scaling an Amazon FBA business to achieve impressive seven-figure revenues, expanding your horizons into multi-channel sales strategies, or preparing meticulously for an acquisition, we at Manay CPA are dedicated to building a comprehensive financial roadmap meticulously tailored to meet your specific business goals. We offer a wide range of services, from accrual-based inventory accounting and detailed COGS tracking to ensuring full compliance with multi-state sales tax regulations and providing strategic tax planning that aligns with your financial objectives. Our firm delivers a holistic approach that supports your e-commerce business at every stage of its journey — from initial startup to ultimate exit planning — ensuring you have the financial clarity and guidance necessary to thrive in today’s competitive landscape.
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Selling online across multiple states creates real tax obligations. We make sure you’re compliant everywhere — and paying only what you owe.
Why Choose Us?
E-commerce sellers across the U.S. trust Manay CPA to handle the financial complexity of selling online.
25+ Years of Experience
Deep, platform-level knowledge of Shopify, Amazon, and multi-channel e-commerce accounting, sales tax, and compliance — across all 50 states.
Proactive Guidance
Year-round sales tax monitoring, monthly reporting, and real-time advisory to keep your business compliant and profitable through every growth phase.
End-to-End Support
From entity formation and bookkeeping to sales tax, COGS management, payroll, and exit planning — one partner for the entire journey.
Our Solutions for E-Commerce Businesses
Overview
E-commerce is one of the fastest-growing sectors in the U.S. economy — and one of the most complex from a tax and compliance standpoint. Between multi-state sales tax obligations, platform-specific revenue recognition rules, inventory capitalization requirements, and nexus thresholds that shift as your business grows, online sellers face a financial landscape that most general accountants are simply not equipped to handle. The deposits that hit your bank account are not your revenue. Your inventory purchases are not immediately deductible. And selling across state lines — whether through your own Shopify store or through Amazon FBA — creates real tax obligations in real jurisdictions. At Manay CPA, we bring 25 years of practical experience and 50-state coverage to e-commerce businesses of every model and size. Our approach goes beyond basic bookkeeping. We serve as your long-term financial partner, providing platform-aware accounting, proactive sales tax compliance, and strategic tax planning that scales with your business.
Every e-commerce business faces a unique compliance profile — shaped by where you sell, how you fulfill, which platforms you operate on, and how fast you’re growing. A Shopify DTC brand has different sales tax responsibilities than an Amazon FBA seller. A multi-channel operator selling through their own website, Amazon, and wholesale has a consolidated reporting challenge that requires specialized financial infrastructure. Manay CPA’s e-commerce team combines deep platform knowledge with AI-augmented workflows and cloud-based accounting tools to deliver accounting, tax, and sales tax compliance services that scale with your operation. We work alongside you to build a clear financial roadmap — one that keeps you compliant in every state, protects your margins, and positions your business for sustainable growth or a successful exit. When you partner with Manay CPA, you gain more than a service provider. You gain a trusted companion who understands how online commerce actually works — and who is invested in your success.
Multi-State Sales Tax Nexus Analysis & Registration
Every e-commerce seller has sales tax obligations — the question is where and how many. Nexus can be triggered by physical presence (warehouse, office, employees, inventory) or by economic activity (exceeding a state’s sales or transaction threshold — typically $100,000 in sales or 200 transactions). For Amazon FBA sellers, inventory stored in Amazon fulfillment centers across the country creates physical nexus in every state where your products sit. For Shopify sellers, you are the merchant of record, meaning you — not the platform — are responsible for collecting and remitting sales tax in every state where you have nexus. We perform a complete nexus analysis, identify every state where you have a collection obligation, and manage your registrations from start to finish.
Sales Tax Collection, Filing & Ongoing Compliance
Once you’re registered, you must collect the correct rate, file returns on the correct schedule, and remit the right amount — in every single jurisdiction. Rates vary not just by state, but by county, city, and special taxing district. Filing frequencies range from monthly to annually depending on your sales volume in each state. We configure your collection settings, manage return preparation and filing, monitor threshold changes, and handle exemption certificate tracking — so your sales tax compliance runs on autopilot while you focus on selling.
Marketplace Facilitator Law Compliance
Since 2019, most states require marketplace facilitators like Amazon, Walmart, Etsy, and eBay to collect and remit sales tax on transactions made through their platforms. This means the marketplace handles sales tax on those orders — but not on sales through your own website, and not necessarily in every state or on every transaction type. The rules vary by state and are constantly evolving. We monitor your marketplace and direct sales across every channel, determine where facilitator laws apply and where they don’t, and manage the filing obligations that remain your responsibility — so you’re never caught in the gap between what the marketplace collects and what you still owe.
Shopify Sellers: Sales Tax Configuration & Compliance
As a Shopify seller, you are the merchant of record for every transaction — which means full sales tax responsibility falls on you. Unlike marketplace sellers, there is no facilitator collecting on your behalf. You must register in every state where you have nexus, configure Shopify’s tax settings to collect the correct rate at checkout, and file returns on time in every registered jurisdiction. We handle the entire lifecycle: nexus determination, state registration, Shopify tax configuration review, return preparation and filing, and ongoing threshold monitoring as your sales grow into new states.
Amazon FBA Sellers: Inventory Nexus & Compliance
Amazon’s FBA program creates a unique and aggressive nexus footprint. When you send inventory to Amazon, it distributes your products across fulfillment centers in multiple states — and in most of those states, the presence of your inventory creates physical nexus, triggering a sales tax collection and filing obligation. Even if marketplace facilitator laws mean Amazon collects on FBA orders, you may still have income tax nexus, annual report filing requirements, and sales tax obligations on non-marketplace sales in those states. We track where your inventory sits, determine your full nexus exposure, and manage every registration and filing that results from it.
Inventory Accounting & Cost of Goods Sold (COGS)
The IRS requires e-commerce businesses that purchase, produce, or sell merchandise to maintain inventory records on an accrual basis. Your inventory spend is not deductible as an expense when purchased — it becomes part of your cost of goods sold only when the product is actually sold. Getting this wrong overstates your deductions, understates your taxable income, and puts you at risk in an audit. We implement proper inventory accounting, track landed costs (product cost, shipping, duties, freight), and calculate COGS accurately across every sales channel and warehouse.
Business Tax Preparation & Strategic Tax Planning
Comprehensive federal and multi-state income tax preparation for e-commerce businesses of every size and structure. We handle entity-level returns, K-1 reporting, and state-specific obligations — while implementing year-round tax strategies including entity structure optimization, owner compensation planning, Section 199A deductions, retirement contributions, and capital expenditure timing to minimize your tax liability legally and sustainably.
Entity Formation & Business Structuring
Choosing the right entity type — LLC, S-Corp, C-Corp, or sole proprietorship — has lasting tax and liability implications for e-commerce sellers. Should you elect S-Corp status to reduce self-employment tax? Should you form in your home state or in a no-income-tax state? We guide you through entity selection, state registration, operating agreements, and post-formation compliance so your business is structured to protect your interests and optimize your tax position from day one.
Multi-Channel Financial Reporting & Profitability Analysis
Selling across Shopify, Amazon, Walmart, Etsy, and wholesale channels creates a complex financial picture. Each platform has different fee structures, settlement timelines, and reporting formats. We consolidate your financial data across all channels into a single, clear view — with channel-level profitability analysis, product-level margin tracking, and KPI dashboards that show you exactly where your money is made and where it’s lost.
International E-Commerce & Cross-Border Tax Compliance
Selling into the U.S. from overseas — or sourcing products internationally and selling domestically — creates cross-border tax, customs, and reporting obligations. For international sellers with a U.S. entity, we manage federal and state tax compliance, FBAR and FATCA reporting, and transfer pricing considerations. For U.S.-based sellers importing goods, we advise on landed cost calculations, duty classification, and the tax treatment of international freight and customs expenses.
Exit Planning, M&A & Brand Acquisition Advisory
E-commerce brands are increasingly attractive acquisition targets — whether through aggregators, private equity, or strategic buyers. The financial groundwork you lay today directly determines your valuation and tax outcome at exit. We provide GAAP-compliant financial statement preparation, seller’s discretionary earnings analysis, tax structuring, and transaction advisory — helping you maximize value and minimize tax liability when the opportunity arrives.
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FAQ
Frequently Asked Questions
I sell on Shopify. Am I responsible for collecting sales tax, or does Shopify handle it?
You are responsible. Unlike marketplace platforms such as Amazon or Etsy, Shopify does not collect or remit sales tax on your behalf. As a Shopify seller, you are the merchant of record — which means you must register in every state where you have nexus, configure your store to collect the correct rate at checkout, and file returns on time in every registered jurisdiction. Shopify provides tax calculation tools, but the legal obligation to register, collect, and remit falls entirely on you. We handle the full lifecycle — from nexus analysis and state registration to Shopify configuration review and ongoing return filing — so you can sell with confidence.
Does Amazon FBA create sales tax nexus in states where my inventory is stored?
Yes. When you use Fulfillment by Amazon, your inventory is distributed across fulfillment centers in multiple states. In most of those states, the physical presence of your inventory creates nexus — triggering sales tax collection and filing obligations. While marketplace facilitator laws mean Amazon collects sales tax on FBA orders in most states, you may still have income tax nexus, annual report filing requirements, and sales tax obligations on any direct-to-consumer sales in those states. We track your inventory distribution, determine your full nexus footprint, and manage every registration and filing that results from it.
What is the difference between marketplace facilitator laws and my own sales tax obligations?
Marketplace facilitator laws require platforms like Amazon, Walmart, Etsy, and eBay to collect and remit sales tax on transactions made through their platform — so for those marketplace orders, the platform handles collection. However, these laws do not cover sales through your own website (Shopify, WooCommerce, etc.), and the rules vary by state. Some states still require you to file returns even if the marketplace collected the tax. Others have specific thresholds and exclusions. We monitor your sales across all channels, determine where facilitator laws apply and where they don’t, and manage the obligations that remain yours.
My accountant records my Shopify/Amazon deposits as revenue. Is that correct?
No — and this is one of the most common and costly mistakes in e-commerce accounting. The deposits from Shopify, Amazon, Stripe, or PayPal that hit your bank account are net settlements — they’ve already had refunds, chargebacks, platform fees, shipping costs, and promotional discounts deducted. Recording these deposits as gross revenue understates your true sales, misclassifies your expenses, and distorts your profitability. We reconcile every platform settlement to its component parts, ensuring your books reflect actual gross revenue, actual fees, and actual net income.
Is my inventory spend tax-deductible when I purchase it?
No. The IRS requires e-commerce businesses that buy and sell merchandise to track inventory on an accrual basis. The cost of your inventory is not deductible as a business expense when purchased — it becomes part of your cost of goods sold (COGS) only when the product is actually sold to a customer. Treating inventory purchases as immediate expenses overstates your deductions and creates a significant audit risk. We implement proper accrual-based inventory accounting, track landed costs (product cost, freight, duties), and calculate COGS accurately across every channel and fulfillment location.
Do you have other questions?
- Talk to an E-Commerce CPA