QuickBooks handles ecommerce well once it is set up correctly and badly when it is not, and the difference is almost entirely about how marketplace data gets in. These are the questions sellers ask most often, answered against what Intuit publishes today rather than what was true two years ago. All prices are US list prices as shown on Intuit’s pricing page in August 2026.
Which QuickBooks plan do I need for an ecommerce business?
Plus, at $140 per month, is the first plan that includes inventory tracking, and inventory tracking is not optional for a product business. Everything below it will let you record sales but not value stock.
The current QuickBooks Online lineup runs Free at $0, Simple Start at $38, Essentials at $85, Plus at $140 and Advanced at $340 per month. Inventory tracking, purchase orders, sales orders and item receipts all begin at Plus. Simple Start connects one sales channel and Essentials connects three; Plus and Advanced connect all of them. If you sell on more than three marketplaces, that alone pushes you to Plus.
Intuit was running a heavy promotional discount when this was written. Budget against list price, because the promotion expires and the subscription does not.
Can QuickBooks connect to Amazon and Shopify directly?
Yes, and for most multi-marketplace sellers the native connection is not sufficient on its own. It brings orders in, but it does not reconcile marketplace settlements, allocate fees by type, or calculate cost of goods sold at the unit level.
The gap shows up first in your bank feed. A single Amazon deposit for $38,015 arrives, representing gross sales, refunds, referral fees, fulfilment fees, storage, advertising and adjustments all netted together. Something has to decompose that into its parts before it hits the ledger. Native connections generally do not.
Should I record marketplace deposits as revenue?
No. That single habit is responsible for more distorted ecommerce books than any other decision.
A deposit is gross sales minus refunds minus fees plus or minus adjustments. Posting the net figure to revenue understates sales, hides every fee category, and makes gross margin percentage arithmetically meaningless because the denominator is wrong. Post gross sales to revenue and each deduction to its own expense account.
What accounts do I actually need?
At minimum: Sales Revenue, Refunds and Returns as a contra-revenue account, Cost of Goods Sold, Inventory Asset, and separate expense accounts for referral or commission fees, fulfilment fees, storage fees, advertising, and settlement adjustments. Add a clearing account per marketplace and per payment gateway.
The clearing account is the part people skip and later regret. It holds sales that have been recognised but not yet paid out, which on a two to five business day settlement lag is always a nonzero balance at month end. Without it, every month boundary misstates.
Cash or accrual?
Accrual, if you carry inventory. It is not really a preference question once stock is involved, because matching cost of goods sold to the period in which the goods sold is the entire point of the method.
The IRS sets out the rules for choosing and applying an accounting method, including the inventory-related requirements, in Publication 538. Talk to your accountant before changing methods, since a change generally requires IRS consent and is not something to do quietly in the software.
How do I get cost of goods sold right?
COGS is units shipped multiplied by the actual landed cost of those specific units, calculated in the period they shipped. Anything else is an estimate, and estimates hide exactly the cost movements you need to see.
Landed cost includes the unit price from the supplier, inbound freight, duties and tariffs, customs brokerage, and any inspection or prep cost. It is not the invoice price. Sellers importing goods have watched landed costs move considerably since the de minimis exemption changes took effect, and a COGS figure built on last year’s landed cost will overstate margin on every unit.
Does QuickBooks handle multiple currencies?
Multiple currencies are available from Essentials upward. Whether that solves your problem depends on how your marketplace reports and whether you want transactions held in the original currency or converted at settlement.
Most sync tools convert to your home currency at the settlement exchange rate, which is usually what you want for reconciliation, because it makes the ledger match the bank. If you need the original currency preserved for supplier or tax reasons, confirm that behaviour before you commit.
What about sales tax?
For marketplace sales in the United States, the marketplace facilitator usually collects and remits the tax, so it never touches your bank account, and it should not touch your revenue account either. Your own website sales are a different matter and are your responsibility.
Nexus rules and thresholds vary by state and change. Check your obligations with your state’s department of revenue and a tax professional rather than relying on software defaults, and treat the general IRS small business guidance as a starting point rather than an answer to a specific filing question.
QuickBooks Online or QuickBooks Desktop Enterprise?
If you need advanced inventory, multi-warehouse tracking or heavy job costing, Desktop Enterprise still does things Online does not. If you need cloud access, multiple simultaneous users and a wide app ecosystem, Online wins.
The practical constraint is your sync tool. A number of well-regarded settlement tools support QuickBooks Online only. Link My Books, for instance, publishes support for QuickBooks Online plans exclusively, with no Desktop option. Confirm your integration path before you choose the accounting platform, not after. ConnectBooks is one of the platforms handling per-SKU marketplace data into QuickBooks Desktop and Enterprise as well as Online, alongside Xero.
How far back can I import historical data?
It varies by tool and it is almost always a paid extension beyond the included window. Plan for it as a project cost rather than assuming it is free.
Ranges published by the major tools sit roughly between 3 months and 24 months of settlement history depending on tier, with additional history purchasable. If you are restating two years of books, price that in before you commit to a platform.
How do I know the sync is working?
Reconcile the clearing account every month and age anything that lingers past one payout cycle. That single control catches most sync failures within thirty days.
Then run two additional checks quarterly. First, divide revenue by units sold and confirm the result matches your average selling price, which proves revenue is gross rather than net. Second, confirm the inventory balance on the balance sheet moved this month without a physical count, which proves cost of goods sold is calculated rather than plugged.
What does the whole stack cost?
QuickBooks Online Plus at $140 per month plus a sync tool is a realistic floor for a multi-marketplace seller carrying inventory. Sync tools published entry pricing ranging from US$29 per month for a single channel up through the low hundreds for platforms that add inventory and SKU-level profit reporting.
Weigh that against what you are currently spending in bookkeeping hours. The IRS estimates the average annual filing burden for entities filing Form 1120-S and related attachments at 60 hours and $4,800, and that is filing alone, on top of whatever monthly close costs you. The arithmetic usually favours automation somewhere between one and three thousand orders a month, but run it on your own numbers rather than taking anyone’s word for it.
Daniel