Introduction
Finding the best accounting software for Amazon sellers is often the difference between a smooth tax season and an IRS audit.
If you sell on Amazon or Shopify, your bookkeeping is 10x harder than a standard business because of the “Deposit Trap.” Amazon sends you a single deposit for $14,000 every two weeks. However, that deposit isn’t just income; it hides $20,000 in sales, minus $4,000 in FBA fees, $1,500 in ad spend, and $500 in refunds.
If you simply record “$14,000 Income” in QuickBooks, your taxes will be wrong. You will overpay the IRS because you forgot to deduct the fees.
In 2026, you cannot do this manually. You need specialized software to bridge the gap. We tested the top 3 tools on the market to see which one actually automates your books.
🏆 Summary: The Top 3 Tools for Sellers
| Software | Best For… | Est. Price | Rating |
| A2X | Best Overall (High Volume) | $29/mo+ | ⭐⭐⭐⭐⭐ |
| Link My Books | Best Value (Xero Users) | $17/mo+ | ⭐⭐⭐⭐⭐ |
| Finaloop | Best “All-in-One” (No QuickBooks) | $245/mo+ | ⭐⭐⭐⭐ |
Why You Need the Best Accounting Software for Amazon Sellers
Many beginners ask, “Can’t I just use QuickBooks?”
The answer is no. QuickBooks alone cannot handle the complexity of e-commerce deposits.
To get accurate books, you generally have two options in 2026:
- The “Connector” Method: You use a tool (like A2X) to connect Amazon to QuickBooks.
- The “All-in-One” Method: You use a specialized platform (like Finaloop) that replaces QuickBooks entirely.
Below, we break down the pros and cons of each approach.
1. A2X (The Gold Standard)
A2X is the tool that professional CPAs trust most. It is widely considered the best accounting software for Amazon sellers who are doing high volume (over $20k/month).
How it works:
A2X sits between Amazon and your accounting software (QuickBooks/Xero). When Amazon sends a payout, A2X automatically generates a Journal Entry that splits the deposit into sales, taxes, refunds, and fees.
Why it wins:
- Accuracy: It matches your bank deposit down to the cent every single time.
- Historical Data: It can go back years and fix your old messy books (crucial if you are facing an audit).
- Cost of Goods Sold (COGS): It tracks your inventory value so you know your true profit margins.
The Verdict: If you are scaling up, A2X is the safest bet. It is the industry standard for a reason.
- Pricing: Starts at $29/month for up to 200 orders.
2. Link My Books (The “Budget” Favorite)
Link My Books was built by Amazon sellers who were tired of A2X’s pricing. It does 90% of what A2X does, but it is often cheaper and easier to set up.
Why it wins:
- The “Tax Wizard”: Setup takes 5 minutes. It asks you a few simple questions (e.g., “Where is your inventory stored?”) and automatically configures your tax rates.
- Benchmarking: In 2026, they added a “Benchmarking” feature that compares your profit margins against other sellers in your niche.
- Xero Integration: While it works with QuickBooks, its integration with Xero is flawless.
The Verdict: If you are a smaller seller or use Xero, this is the best value for money.
- Pricing: Starts at $17/month (vs A2X’s $29).
3. Finaloop (The AI Disrupter)
Both A2X and Link My Books require you to also pay for QuickBooks ($35+/mo).
Finaloop is different. It replaces QuickBooks entirely.
How it works:
Finaloop is “Real-Time” accounting software designed specifically for DTC (Direct-to-Consumer) brands. Instead of waiting for the month to end, it connects to your bank and Shopify store to give you a Live P&L every single day.
Why it wins:
- No QuickBooks Needed: You save money and hassle by cancelling your QuickBooks subscription.
- Inventory Sync: It tracks your inventory levels in real-time across Shopify and Amazon.
- Human Support: Their plans include a team of human bookkeepers who review your books for accuracy.
The Verdict: Perfect for Shopify Brands who want a modern dashboard and hate QuickBooks.
- Pricing: Starts at ~$245/month, but remember: you don’t need to hire a separate bookkeeper or pay for QuickBooks.
Comparison: A2X vs. Link My Books
| Feature | A2X | Link My Books |
| Pricing | Higher ($29 – $69+) | Lower ($17 – $35+) |
| Setup Time | Moderate (30 mins) | Fast (10 mins) |
| Benchmarking | No | Yes |
| Best For | Large FBA Sellers | Small-Med Sellers |
Conclusion: Which One Should You Buy?
Choosing the right tool depends on your business model:
- Choose A2X if: You are an Amazon FBA seller scaling up and want the tool that every CPA trusts.
- Choose Link My Books if: You want a simple, affordable tool that just works (especially for Xero users).
- Choose Finaloop if: You run a Shopify brand and want to automate everything (and fire your bookkeeper).
Ready to clean up your books?
Don’t wait until April 14th.
