An Amazon-heavy seller who runs fulfillment software has two cost paths for the same SKU, and the general ledger needs both kept apart. Units that ship through FBA carry inbound freight to Amazon, a fulfillment fee at sale, and monthly storage. Units that ship merchant-fulfilled carry a label, in-house pick and pack, and your own warehouse's cost. Same product, different landed cost, different cost of sale, different margin. The fulfillment software knows which path each unit took. The handoff to accounting is where that knowledge either reaches the books or gets averaged away.
Nineyard describes itself on nineyard.com as modular ecommerce software for marketplace sellers, with separate modules for inventory and forecasting, FBA shipment management, inventory management, repricing, and business analysis. ConnectBooks connects Nineyard data to QuickBooks or Xero. This article is about what the ledger should receive from that kind of software and what it should compute on its own.
Inbound. Freight from your warehouse or supplier to an Amazon fulfillment center is a cost of getting inventory to where it sells. Capitalize it into the landed cost of the units sent, or expense it, by policy. Capitalizing is the more accurate answer for margin, since it puts the cost in the month of the sale rather than the month of the shipment.
At sale. Amazon deducts a referral fee and an FBA fulfillment fee from each order. These appear on the settlement report, not in the fulfillment software, and they post to the ledger as expenses when the settlement reconciles. Amazon publishes its fee schedules on sellercentral.amazon.com; the figures below are illustrative, not quoted.
Monthly. Storage fees, and for aged units the surcharges, arrive on the settlement as non-order charges. They are a cost of holding inventory at Amazon and belong on their own expense line so they can be tracked by SKU.
At sale. Amazon still takes the referral fee. Fulfillment is yours: a carrier label bought through shipping software, packaging, and the labor to pick and pack. Labels are per-order costs with an order reference. Labor and packaging are usually allocated at a standard rate per unit.
Monthly. Your warehouse rent and staff, whether allocated to units or left as overhead.
The two paths produce different unit margins for an identical product, and a seller deciding how much of a SKU to send to FBA needs both numbers side by side.
FBA inventory is your inventory. It sits on your balance sheet at your cost until it sells, even though Amazon holds it. In the fulfillment software and in the ledger, Amazon's fulfillment centers are a warehouse location like any other, with a third location for units in transit to Amazon.
The counts drift. Amazon receives short, loses units, damages units, and later reimburses some of them. Your fulfillment software's FBA count and Amazon's own inventory ledger will not match at month end, and the ledger's implied count (receipts minus COGS relief) will match neither. Reconciling the three is a monthly task, and the mechanics of it, report by report, are in how to reconcile Amazon FBA inventory to your books.
Illustrative numbers. One SKU, landed cost $14.00 at your warehouse, selling at $34.99 with a 15 percent referral fee. Fulfillment fee and storage figures are made up for the example.
Start of month: 1,000 units. The seller sends 700 to FBA and keeps 300 for merchant fulfillment. Inbound freight to Amazon is $560, capitalized: $0.80 per unit, so the FBA units carry $14.80.
FBA sales: 400 units
Merchant-fulfilled sales: 100 units
FBA won this month by 6 points per unit, and the storage line shows where that lead shrinks if the units sit. A seller who averaged the two paths would see 500 units at a blended $9.12 contribution before storage and would not know that the merchant-fulfilled units are 6 points worse, or why.
Month-end count
The fulfillment software says 300 FBA units remain. Amazon's inventory report says 296. Four units are missing: two Amazon recorded as damaged in the warehouse, two it cannot find.
The ledger's inventory count for the SKU at month end: 296 at FBA at $14.80, 200 at your warehouse at $14.00.
A removal order the following month
The seller pulls 50 slow units back from FBA ahead of storage surcharges. In the fulfillment software that is a transfer from the Amazon location to your warehouse. In the ledger the units keep their $14.80 basis; the inbound freight capitalized on the way out does not come back off. Amazon's removal fee is an expense in the month charged, on the same line as storage, not a reduction of inventory value. Your warehouse now carries two cost layers for one SKU, 200 at $14.00 and 50 at $14.80, and FIFO decides which sells first.
Monthly, on the close, is the minimum. Three checks in order.
Sellers moving high volume through FBA check step two weekly, because a receiving shortfall found four weeks late is much harder to claim.
From the fulfillment software: units shipped by SKU by path, inbound shipment quantities and freight, location counts at month end, label cost with order references for merchant-fulfilled orders. From the Amazon settlement: referral fees, fulfillment fees, storage, reimbursements, refunds. From the ledger's own records: landed cost layers and FIFO relief.
ConnectBooks reconciles each settlement into QuickBooks or Xero at the transaction level and tracks inventory by warehouse, including units in transit, with FIFO valuation and landed cost allocation. Nineyard data connects to it as a source. Two paths in, two margins out, one balance sheet that knows where every unit is.
Running an e-commerce business comes with plenty of challenges, but ConnectBooks is here to make your life easier. With real-time insights, seamless integrations, and detailed tracking of your profitability and inventory, you can stay ahead of the game. Whether you’re selling on Amazon, Shopify, Walmart, TikTok or eBay, ConnectBooks helps you manage your finances with 100% accuracy and confidence, so you can focus on growing your business.
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