Smart Bookkeeping for Smart Sellers
Use this practical inventory reconciliation guide to compare physical counts, warehouse reports, marketplace quantities, accounting balances, stock adjustments, damaged goods, obsolete products, write-downs, and cost of goods sold. Built for Amazon sellers, Shopify brands, marketplace sellers, and bookkeepers who want cleaner inventory numbers every month.
Physical Counts, Write-Downs & Adjustments is an inventory reconciliation guide for sellers and bookkeepers who need inventory balances they can trust. Instead of relying only on a marketplace dashboard or an accounting software balance, this guide helps you connect real stock on hand with SKU reports, supplier invoices, warehouse movement, sales activity, returns, write-downs, and cost of goods sold.
Inventory is one of the easiest areas for an eCommerce business to misstate. A seller may have products at Amazon FBA, a 3PL warehouse, a small office, a supplier location, a prep center, or in transit. Sales can happen on Amazon, Shopify, Walmart, eBay, Etsy, TikTok Shop, and wholesale channels. Returns may be resellable, damaged, disposed, replaced, or never received back into stock. If those movements are not reconciled, the profit and loss statement can look better or worse than reality.
A proper inventory reconciliation does more than count boxes. It explains the difference between the quantity shown in your inventory system and the quantity that actually exists. It also checks whether products are recorded at the right value. Damaged products, obsolete SKUs, expired items, slow-moving bundles, and goods that cannot be sold at normal prices may require review before the month is closed. The goal is to make inventory, COGS, gross margin, and tax-ready reports more reliable.
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This guide is designed for online sellers, inventory managers, accountants, and bookkeepers who want a repeatable way to close inventory each month. A good inventory close helps answer important questions: How many units do we really have? Which SKUs are missing? Which products are damaged? Which items are unsellable? Are landed costs complete? Is COGS aligned with units sold? Are write-downs supported by evidence?
Compare physical counts, FBA reports, 3PL reports, warehouse logs, and inventory software so units on hand are not guessed.
Document damaged, expired, obsolete, returned, or unsellable items before reducing the inventory value in your books.
Create a clean adjustment log for shrinkage, receiving errors, bundle issues, supplier shortages, transfers, and corrections.
Review COGS, landed costs, freight, duties, prep fees, and product costs so profit is not overstated or understated.
Use reconciled inventory to produce better balance sheets, profit and loss reports, SKU profitability, and tax-ready records.
Save count sheets, photos, warehouse exports, approvals, and notes so future questions are easier to answer.
Use the checklist below as a working version of the guide. The timing is a practical target for a clean account with organized records. A seller with multiple warehouses, high SKU volume, large FBA activity, wholesale inventory, or old cleanup issues may need more time. The order of the checklist still helps keep the process controlled.
Inventory reconciliation gives your business a reliable bridge between real-world stock and financial reporting. Without a recurring process, small differences can hide for months. Products may be missing, damaged units may still appear as sellable, obsolete SKUs may stay at full cost, returned items may be counted twice, and COGS may not match actual units sold.
A strong inventory reconciliation works best when the steps happen in the right order. If you post adjustments before checking the cutoff date, you may correct the wrong month. If you review COGS before confirming quantities, gross margin may still be unreliable. If you write down inventory without documentation, future review becomes difficult. This framework moves from count evidence to accounting entries and final reports.
Gather count sheets, warehouse reports, FBA exports, 3PL files, return bins, damaged stock logs, and in-transit details.
Match physical quantities to inventory software, marketplace reports, purchase orders, receiving records, and SKU ledgers.
Identify the reason for differences: shrinkage, returns, bundles, supplier shortages, receiving errors, transfers, or disposal.
Review unit cost, landed cost, freight, duties, prep fees, discounts, obsolete stock, damaged units, and write-down needs.
Post approved quantity adjustments, value adjustments, COGS corrections, reclassifications, and open item notes.
Save final inventory valuation, adjustment summary, write-down support, balance sheet, P&L, and monthly reconciliation file.
A physical count is the foundation of inventory reconciliation. The count should include every place where the business owns inventory, not only the main warehouse. For online sellers, that may include Amazon FBA, a third-party logistics provider, a home office, a retail shelf, a prep center, samples, return bins, defective items, wholesale cartons, goods in transit, and products waiting for inspection.
The most important control is the cutoff date. If a count is performed on June 30, the team must understand which sales, receipts, returns, transfers, and disposals belong before June 30 and which belong after June 30. Without a clean cutoff, the same shipment can be counted in one place and recorded in another, or missed entirely.
A write-down is used when inventory is still on hand but its recorded value is higher than the amount the business expects to recover. This can happen when products are damaged, expired, missing packaging, out of style, slow-moving, returned in poor condition, restricted by marketplace rules, or no longer sellable at normal prices. The write-down should never be a random guess. It should be supported by count details, SKU notes, sales data, disposal evidence, replacement cost, or other clear support.
For sellers, write-downs are often discovered during physical counts and return reviews. A bin of customer returns may still be listed as sellable. A discontinued SKU may sit in a warehouse for a year. A private-label product may lose value after a packaging change. A seasonal product may be worth less after the season ends. These are operational issues, but they also affect the balance sheet and the profit and loss statement.
| Inventory Issue | What to Review | Possible Bookkeeping Action |
|---|---|---|
| Damaged Products | Photos, return notes, warehouse inspection, customer complaint history, disposal notes | Reclassify as damaged inventory, write down value, or remove if disposed with approval. |
| Obsolete SKUs | Last sale date, listing status, replacement product, market price, liquidation estimate | Review for write-down based on expected recovery and save management notes. |
| Expired Goods | Expiration date, lot code, marketplace restriction, disposal requirement, supplier credit | Write down or remove from inventory if no longer sellable, with support. |
| Missing Units | Count sheets, shipment records, FBA adjustments, 3PL logs, receiving reports | Post shrinkage or correction entry after investigation and approval. |
| Overstated Cost | Supplier invoices, freight bills, duties, discounts, landed cost worksheet | Correct unit cost, landed cost, inventory value, and COGS if needed. |
Inventory adjustments should explain what changed and why. A quantity adjustment changes the number of units in the inventory records. A value adjustment changes the dollar value of inventory. A COGS adjustment corrects the cost recognized for products sold. A reclassification moves costs between accounts when the original entry was posted to the wrong place. Good reconciliation separates these categories so the final reports are easier to review.
For example, if 25 units are missing from a warehouse count, the business may need a shrinkage adjustment. If the quantity is correct but the unit cost is wrong, the business may need a value correction. If purchases were recorded as expenses instead of inventory, the business may need a reclassification. If sold units were not relieved from inventory, the business may need a COGS entry. Each adjustment should have a reason, support, approval, and posting date.
Inventory reconciliation is closely tied to cost of goods sold. If inventory quantities are wrong, COGS may also be wrong. If landed costs are incomplete, gross margin may be overstated. If purchases are expensed immediately, the month may show a loss when inventory was actually still on hand. If COGS is not recorded when products are sold, profit may look too high.
A useful month-end review compares sales units, inventory reductions, COGS, gross margin percentage, purchase activity, and ending inventory value. Large margin changes should be explained. A sudden improvement may be real, but it may also mean COGS was missed. A sudden drop may reflect write-downs, freight cost changes, supplier price increases, or a coding error. This is why inventory reconciliation should be part of the close, not a separate year-end project.
Bookkeeping note: this page is educational and does not replace tax or accounting advice. Inventory accounting methods, write-down treatment, and tax reporting can depend on your facts, accounting method, entity type, and CPA guidance.
A clean inventory reconciliation folder makes it easier to review adjustments later. It also helps when your CPA asks for support, when a warehouse dispute comes up, when a supplier claim is pending, or when you need to explain gross margin changes. The folder should be simple, consistent, and saved every month.
| Folder Section | Documents to Save | Why It Matters |
|---|---|---|
| Physical Count | Count sheets, location reports, SKU lists, signed count review, discrepancy notes | Supports actual units on hand and explains count differences. |
| Marketplace & Warehouse | Amazon FBA reports, 3PL reports, Shopify inventory exports, transfer logs | Connects external platforms to internal inventory records. |
| Purchases & Landed Cost | Supplier invoices, freight bills, duties, prep fees, packaging, landed cost worksheets | Supports unit cost and inventory valuation. |
| Write-Down Support | Photos, obsolete SKU review, disposal notes, return inspection notes, approval records | Supports reductions for damaged, expired, obsolete, or unsellable stock. |
| Final Reports | Inventory valuation, adjustment summary, COGS report, gross margin review, balance sheet, P&L | Creates a final month-end snapshot of inventory and profit impact. |
Most inventory problems come from skipped review steps. A seller may count warehouse stock but forget damaged returns. A bookkeeper may post purchases directly to expenses without checking inventory on hand. A warehouse may report units by location while the accounting system reports units by SKU. A write-down may be booked without photos or approval. These mistakes make reports less reliable and can create cleanup work later.
The Physical Counts, Write-Downs & Adjustments guide is useful for anyone responsible for inventory accuracy, monthly reporting, or eCommerce bookkeeping. It is especially helpful when products move through multiple locations or when sellers need better support for COGS, write-downs, shrinkage, and SKU profitability.
Use it to reconcile FBA inventory, stranded inventory, removals, lost units, reimbursements, returns, and SKU costs.
Use it to compare Shopify inventory, 3PL stock, returns, bundles, product costs, and warehouse adjustments.
Use it as a repeatable client workflow for inventory close, COGS review, write-down support, and reporting.
Use it to create cleaner count sheets, adjustment logs, approval notes, and month-end inventory support.
Continue building a cleaner bookkeeping system with related Seller Bookkeeping resources. These internal pages help sellers understand Amazon accounting, monthly close, product profitability, bookkeeping decisions, and tax-ready recordkeeping.
Learn how Amazon sellers should track settlements, FBA fees, refunds, reimbursements, inventory, COGS, and SKU profitability.
Use a month-end bookkeeping checklist to organize payouts, bank reconciliation, inventory, reports, and tax-ready records.
Review how product costs, fees, refunds, advertising, and fulfillment costs affect real profit by SKU or ASIN.
Request help with inventory reconciliation, monthly bookkeeping, ecommerce cleanup, COGS review, and tax-ready reports.
For general inventory and recordkeeping context, business owners can review IRS Publication 538 and the IRS recordkeeping guide. External guidance is useful, but your own inventory reconciliation process should be built around your sales channels, warehouses, accounting software, CPA guidance, and reporting goals.
Seller Bookkeeping helps eCommerce sellers review inventory balances, reconcile marketplace and warehouse reports, document write-downs, clean up COGS, prepare monthly reports, and reduce year-end surprises. A consistent inventory reconciliation process gives you cleaner numbers and better decisions.
Schedule Free ConsultationInventory reconciliation is the process of comparing physical stock, inventory software, marketplace reports, warehouse reports, supplier invoices, accounting balances, sales activity, returns, and adjustments so the inventory balance is accurate.
Many sellers do a full physical count at year end and smaller cycle counts monthly or quarterly. Inventory-heavy businesses, fast-moving SKU sellers, and sellers using FBA or 3PL warehouses may need more frequent review.
An inventory write-down reduces the recorded value of products when they are damaged, obsolete, expired, unsellable, or worth less than their recorded cost. The write-down should be supported by notes, count records, photos, and approval.
Common causes include physical count differences, shrinkage, warehouse errors, receiving mistakes, customer returns, damaged products, FBA lost or found inventory, supplier shortages, bundles, kits, transfers, and unit cost corrections.
Inventory businesses usually track product purchases as inventory until the products are sold, then recognize cost of goods sold. Tax treatment and accounting method decisions should be reviewed with a qualified accountant or CPA.
A write-down generally reduces inventory value and increases an expense or COGS-related account, which can reduce profit for the period. The exact treatment depends on your accounting policy and the reason for the adjustment.
Useful reports include inventory valuation, SKU quantity export, adjustment summary, physical count sheets, write-down support, COGS report, gross margin review, balance sheet, profit and loss statement, and open-items notes.
Yes. Seller Bookkeeping can help with inventory reconciliation, FBA and 3PL report review, landed cost checks, COGS cleanup, write-down support, monthly bookkeeping, and tax-ready reporting for eCommerce sellers.