You log into Seller Central and see you made $10,000 in sales this week. You feel great.
Then you check your bank account, and Amazon has only deposited $6,432.
Panic sets in. Where did the money go? Did Amazon make a mistake?
Welcome to the “Deposit Trap.”
For Amazon FBA sellers, “Sales” and “Deposits” are two completely different numbers. Amazon deducts dozens of fees—shipping, ads, refunds, storage, reserves—before sending you a single cent.
If you are trying to do your bookkeeping manually by downloading spreadsheets, you are likely doing it wrong. And with the new “DD+7” payment policy hitting in March 2026, understanding your cash flow has never been more critical.
Here is the definitive guide to Amazon FBA bookkeeping in 2026, and a head-to-head comparison of the tools that solve this nightmare: A2X vs. Link My Books vs. Webgility.
The “Deposit Trap”: Why Manual Amazon FBA Bookkeeping Fails
Most new sellers try to book their revenue based on the cash that hits their bank account. This is called Cash Basis Accounting.
- Problem: It gives you zero visibility into your actual costs.
- Example: If you spent $3,000 on ads but they were deducted from your payout, you might think your profit margins are healthy when you are actually losing money.
The 2026 Challenge: “DD+7” Policy
Starting March 12, 2026, Amazon will hold your funds for 7 days after delivery (DD+7).
This means a sale made in January might not be paid until February.
If you use Cash Basis accounting, your January books will look terrible (high ad spend, low income) and your February books will look artificially amazing.
** The Solution: Accrual Accounting**
You need to record the sale when it happens, not when you get paid. This is impossible to do manually with thousands of orders. You need a “Connector Tool.”
The Contenders: Best Amazon Accounting Software 2026
We have analyzed the top tools that connect Amazon Seller Central to QuickBooks Online or Xero.
1. A2X (The Industry Standard) 🏆
A2X is the gold standard for accountants. It takes the messy Amazon settlement reports and turns them into clean “Journal Entries” in QuickBooks.
- Best For: Sellers who want 100% accuracy and audit-proof books.
- Pros: Perfect accrual accounting. Handles international taxes (VAT/GST) flawlessly.
- Cons: Expensive for multi-channel sellers (you pay per channel). Does not give “Order Level” details (it posts summaries).
2. Link My Books (The Rising Star) ⭐
Popular in the UK and Europe, Link My Books is growing fast in the US due to its transparent pricing and ease of use.
- Best For: Small to Mid-sized sellers who want simplicity.
- Pros: Cheaper (pricing includes all channels). Fantastic “Guided Setup” wizard. Handles COGS (Cost of Goods Sold) automatically.
- Cons: Slightly less robust for massive enterprise sellers compared to Webgility.
3. Webgility (The Enterprise Beast) 🏢
Webgility is more than just accounting; it’s an operations platform.
- Best For: Omnichannel brands selling on Amazon, Shopify, Walmart, and eBay who need inventory syncing.
- Pros: Order-level details (records every single customer name/address). Syncs inventory across channels.
- Cons: Expensive and complex. Overkill for pure FBA sellers.
Comparison Table: Which One Do You Need?
| Feature | A2X | Link My Books | Webgility |
| Accounting Method | Summary (Journal Entry) | Summary (Invoice) | Detail (Order Level) |
| Price Model | Per Channel (Expensive) | By Volume (Cheaper) | Flat/Tiered (High) |
| COGS Tracking | Basic | ✅ Advanced | ✅ Advanced |
| Inventory Sync | ❌ No | ❌ No | ✅ Yes |
| Ease of Setup | Hard (Needs Accountant) | Easy (DIY) | Hard (Complex) |
| Best For… | Accuracy Purists | Value Seekers | Big Brands |
COGS: The Missing Piece of the Puzzle
Revenue is vanity; Profit is sanity.
To know your profit, you must track COGS (Cost of Goods Sold).
Most generic accounting software (QuickBooks) is terrible at inventory.
- A2X & Link My Books allow you to upload a “Cost Price” for each SKU.
- When Amazon sells a widget, the software automatically tells QuickBooks: “Reduce inventory asset by $5 and increase COGS expense by $5.”
Without this automation, you will never know your true monthly profit.
Summary: What Should You Buy?
- Choose [Link My Books] if: You sell on multiple channels (Amazon + Shopify + eBay) and want to save money on subscription fees. The interface is friendlier for non-accountants.
- Choose [A2X] if: You have a professional CPA who demands “Journal Entries” and strict adherence to GAAP standards.
- Choose [Webgility] if: You need to sync inventory levels between your Shopify warehouse and Amazon FBA to prevent overselling.
Now that your books are automated, ensure you aren’t paying sales tax out of your own pocket. Read our guide on Amazon FBA Sales Tax Nexus or check the Ultimate Tax Deductions Checklist to save even more money.