Financial Support Built for New York's E-commerce Sellers
Selling online out of New York brings a level of financial complexity most general accountants aren't equipped to navigate. NexusWorks LLC handles bookkeeping, sales tax compliance, and fractional CFO work specifically for e-commerce brands, giving sellers a clear financial picture and one team instead of three disconnected vendors.
New York's dual nexus test trips up sellers who only track one number
What lands in your bank account from Amazon rarely matches what you actually sold
Margins look stronger than they are when COGS is calculated incorrectly
We also support e-commerce sellers in California, Texas, Florida, Washington, and Tennessee.
The Recurring Financial Struggles of New York Sellers
Generalist accountants weren't built for the pace of online retail. The same problems show up repeatedly among New York-based sellers:
Amazon shifts inventory between fulfillment centers constantly, leaving sellers unsure exactly which states carry a nexus obligation.
Bank deposits from Amazon and Shopify rarely reflect what was actually sold, making monthly reconciliation a persistent headache.
COGS gets miscalculated when landed cost, prep fees, and FBA charges aren't tracked correctly from the outset.
Amazon's tax collection covers marketplace orders only New York still expects direct registration and remittance on everything sold outside that channel.
Bookkeeping and tax planning run as separate functions, so deductions get missed and quarterly estimates rely on stale numbers.
Selling across several channels without one consolidated view means no one has a clear read on last month's actual profitability.
A bookkeeper working alone can’t solve this. Neither can a tax preparer operating in isolation. It requires one coordinated system watching all of it together.
What Makes New York's Nexus Rules Uniquely Complicated
The Combined Threshold Most Sellers Get Wrong
New York doesn't use a single trigger the way most states do. Nexus requires crossing both $500,000 in sales and 100 separate transactions within the preceding four sales tax quarters - not a calendar year, and not either threshold alone. A seller with high revenue from a handful of large orders can stay under the transaction count, while a seller with modest revenue from many small orders can cross it early. Both conditions have to be satisfied.
Physical Nexus From FBA Storage Applies Regardless of the Dual Threshold
Storing inventory in a New York fulfillment center creates physical nexus the instant it arrives, independent of the $500,000 and 100-transaction test entirely. Marketplace facilitators like Amazon collect and remit on their own orders, but direct sales through a Shopify store or website remain the seller's obligation, and critically, those marketplace sales still count toward the seller's own dual threshold calculation.
Combined Rates Reach 8.875% in New York City
The state rate is 4%, with New York City and county additions bringing the total to 8.875% in Manhattan and similar levels across the other boroughs. Rates vary meaningfully outside the city. New York is destination-based, so the applicable rate depends entirely on where the customer receives the order.
Multi-Channel Sellers Are the Department's Primary Audit Focus
Because the dual threshold makes it easy to under-calculate nexus by looking only at direct sales, New York has increased scrutiny on sellers who mix marketplace and direct-to-consumer revenue. Sellers who register late or miscount transactions across channels are the most common audit targets, with lookback periods extending several years.
This isn't a tax explainer. These are specific, active risks your financial team should already be managing.
How NexusWorks Supports New York E-commerce Sellers
Reconciliation That Covers Every Channel
Each month, we tie revenue, fees, refunds, and chargebacks from Amazon, Shopify, Etsy, and anywhere else you sell back to your actual bank deposits. Reserve holds and mid-cycle payouts distort settlements on their own — we clean it up into financials that reflect what you truly earned.
Nexus Tracking Built for New York's Dual Test
We register with the New York State Department of Taxation and Finance and track both your revenue and transaction count together against the $500,000-and-100-transaction threshold, rather than watching either number in isolation. Since marketplace sales count toward your own nexus figure here, we monitor combined channel activity so you know exactly when registration becomes required.
COGS and Inventory Accounting Matched to Your Fulfillment Model
Whether you run FBA, third-party logistics, or in-house fulfillment, we build inventory accounting around it. Freight, duties, and prep costs roll into landed cost, so margins reflect what products actually cost to deliver.
Fractional CFO Work as Revenue Scales
Once revenue stabilizes, decisions get more complex inventory purchasing, supplier terms, ad spend efficiency, cash flow timing. We model all of it: forecasting, inventory financing analysis, channel-level P&L, and reporting built for investors or lenders.
Ready to Get Your E-commerce Finances Under Control?
If your brand has grown past the point where your current financial setup can keep up, that gap is costing you money in missed deductions, incorrect filings, and decisions made on inaccurate numbers. Our team reviews your platform reconciliation, New York tax exposure, and entity structure and tells you exactly what needs to change.
Why New York Sellers
Choose NexusWorks
E-commerce sits at the center of our practice, not on the periphery. We understand how Amazon settlements actually work.
Why Shopify payouts diverge from real revenue, and how nexus builds across channels and states as a brand scales.
Bookkeeping, tax, and CFO functions live inside one team, keeping your financial picture consistent with nothing falling through the gap between accountant and advisor.
Everything runs remotely through QuickBooks, Xero, and secure portals, with pricing that stays transparent from the first conversation.
Request An Instant Consultation
Or Call Us Today At +1 310-810-1790
Frequently Asked Questions
Amazon's collection only covers orders placed through Amazon itself. Sales through your own Shopify store or website remain your responsibility, and those marketplace sales still count toward whether you've crossed New York's dual threshold. A CPA also manages income tax, COGS accuracy, and multi-channel nexus tracking that Amazon's system never addresses.
Yes. Physical nexus from FBA storage applies immediately and independently of the economic thresholds. The dual $500,000-and-100-transaction test is a separate path to nexus that applies even without any physical presence in the state.
Bookkeeping covers daily recording, platform reconciliation, and expense sorting. Accounting builds on that into financial statements, tax strategy, and profitability insight. Both need to work together for e-commerce sellers, since platform fees and inventory costs require treatment that general bookkeeping typically misses.
Yes, completely. We connect directly to your platforms and bank accounts through QuickBooks, Xero, and secure portals, deliver monthly reports, and manage every New York and multi-state filing without an in-person requirement.
We build landed cost from the ground up purchase price, freight, import duties, prep fees then match it against monthly units sold for an accurate gross margin. FBA storage fees, disposal charges, and shrinkage all factor in too, so your P&L reflects the true cost of selling through Amazon.