Best Amazon FBA Accounting and Inventory Software: 2025 Edition

It’s the end of the month. You’re buried in 5 spreadsheets, trying to match your payouts, track lost inventory, and figure out why Amazon still hasn’t reimbursed you for those damaged units. 

Meanwhile, your inbox pings with a reminder about sales tax filings, and you’re still not sure which states you even owe.

If you’re an Amazon FBA seller, this chaos is all too familiar.

Amazon’s ecosystem is complex. Between ever-changing fees, multi-state sales, and shifting inventory levels, using a generic accounting tool only leads to more confusion and mistakes. 

You need software built specifically for Amazon sellers: tools that sync directly with your Seller Central account, break down your actual profits, and help you avoid compliance headaches.

This guide breaks down exactly what you need to know and what tools actually work for sellers like you. 

Let’s help you choose the right accounting and inventory stack for a smoother, smarter FBA operation.

Best Amazon FBA Accounting and Inventory Software at a Glance

Why Amazon FBA Sellers Need Specialized Accounting and Inventory Software

When Maya, an Amazon FBA seller from Toronto, filed her taxes last year, she thought everything was under control. 

However, when her accountant reviewed the files, they realized Maya had counted her gross sales without subtracting Amazon’s fees, shipping charges, or returns. 

The result? A significantly inflated revenue figure and a bigger tax bill than necessary. Maya isn’t alone.

Amazon FBA sellers face a unique set of financial challenges that generic tools like Excel or traditional accounting software just aren’t built to solve.

Common Financial and Inventory Challenges for FBA Sellers

1. Tracking Amazon fees, reimbursements, refunds, and advertising costs

Every FBA transaction is packed with hidden fees. If you’re not syncing directly with Amazon’s settlement data, it’s easy to misreport or miss what you actually earned.

2. Delays in payouts and understanding net revenue

Amazon pays out every two weeks, but what lands in your bank account often doesn’t match your expectations. 

Without apparent reconciliation, understanding what’s profit vs. pending vs. deducted becomes a guessing game.

3. Poor visibility into COGS (Cost of Goods Sold)

If you sell across multiple SKUs or adjust pricing frequently, your true profitability is always in flux. Manual tracking can’t keep up with inventory fluctuations or fees tied to specific products.

🔖 Related Read: How Do I Calculate Cost of Goods Sold (COGS)?

Why Generic Tools Fall Short

• Excel doesn’t auto-sync with Amazon. You’ll spend hours copying and pasting, and still risk errors in revenue recognition, fees, or inventory levels.

• Off-the-shelf accounting software wasn’t built for e-commerce. Tools not tailored to FBA ignore things like real-time stock depletion, fulfillment costs, or multi-channel complexities.

Using the wrong tool can cost you thousands in misfiled taxes, lost reimbursements, or inventory shortfalls that stunt your growth.

Key Features to Look for in FBA Accounting and Inventory Software

Not all accounting tools are built equally, especially when it comes to the complexity of Amazon FBA. 

If you’re choosing software to support your FBA business, here’s your must-have buyer’s checklist.

Each of these features solves a very real (and costly) pain point.

✅ Amazon API Integration

You need real-time access to settlement reports, shipping fees, reimbursements, and refunds directly from Amazon. 

Manual uploads or disconnected platforms can cause data lags and missed transactions.

Also, if your software requires CSV uploads from Seller Central, it’s already outdated.

✅ Multi-Channel and Multi-Currency Support

Selling on Amazon US, CA, and Europe? Also listing products on Shopify or Walmart? Your tool should consolidate performance across channels and currencies without making you run separate reports.

Also, if your dashboard only shows Amazon data and ignores your other stores, you’re not getting the full picture.

✅ Inventory Syncing and COGS Tracking

Inventory drives your profitability. Your software should automatically track how much product you’ve sold, what it cost, and what’s left without relying on clunky manual spreadsheets.

If your tool can’t break down COGS per SKU, you’re likely guessing your profit margins.

✅ Payout and Fee Reconciliation

Amazon’s bi-weekly payouts rarely match your actual sales.

If you’ve ever looked at your bank deposit and thought “Where did all my money go?” this is why.

With reimbursements, ad spend, and fees deducted behind the scenes, you need software that breaks it down clearly.

✅ Tax-Ready Reports & Sales Tax Features

Your tool should help prepare accurate financial reports, support quarterly estimated tax filings, and track sales tax obligations across states where you have nexus.

If your reports aren’t accepted by your tax preparer, or if you’re scrambling at tax time, it’s not working.

For instance, tools like doola don’t just show you how much you made, they help you understand how much you keep, what to reinvest, and how to stay compliant.

Top 4 Accounting Software for Amazon FBA Sellers

Choosing the right accounting software can be a game-changer for Amazon sellers. Below is a breakdown of top accounting tools in 2025, including their key features, pricing, and ideal customers.

1. doola: An All-in-One Powerhouse

doola isn’t just software, it’s your finance team in a box.

From reconciling every Amazon fee to filing your federal and state taxes, it combines powerful bookkeeping tech with real CPAs and e-commerce experts handling everything for you.

Best for: Founders who don’t want to worry about books, taxes, or compliance, especially if selling on Amazon or other e-commerce platforms.

Key Features:

• Native support for Amazon FBA reports (Amazon-specific transaction breakdowns)

• Full federal and state tax filings (1040, 1120, 1120-S, 1065, 5472, K-1s, etc.)

• Sales tax compliance + reseller certificate setup

• 1099 filing to avoid $250-per-form IRS penalties

• Inventory and COGS tracking synced to Amazon, Shopify, Etsy, and Stripe

• Dedicated bookkeeper + expert tax prep (real CPAs managing your filings)

• Integrated books + tax support

• Catch-up filings to avoid $25K IRS penalties

Pricing:

$329/month, which includes bookkeeping, tax filing, sales tax setup, registered agent, EIN, and more.

Pros:

✔️ All-in-one compliance + accounting platform

✔️ Expert CPA filings = no DIY stress

✔️ Built specifically for U.S. and international Amazon sellers

✔️ Zero software maintenance or setup required

Other tools still require you (or your accountant) to know how to properly categorize FBA fees, track inventory costs, and file taxes across multiple states.

With doola, you’re not guessing.

Sign up with doola and get started in under 5 minutes. Scale your Amazon business without spreadsheets, stress, or IRS penalties!

2. QuickBooks Online

Best for: Sellers scaling beyond $500K/year who need internal financial controls, advanced reporting, and payroll tools.

Key Features:

• Integration with A2X for Amazon settlements

• Highly customizable chart of accounts

• Built-in invoicing, expense tracking, and payroll

• Syncs with 650+ third-party tools

Pros:

✔️ Ideal for in-house finance teams or accountants

✔️ Powerful reporting + budgeting features

Cons:

🚩 Setup and reconciliation require experience

🚩 Doesn’t support Amazon natively and needs A2X

🚩 No included CPA/tax filing

Pricing:

$35/month (Essentials) to $250/month (Advanced)

3. Xero

Best for: International or budget-conscious sellers who want a clean UI and simple bookkeeping workflows.

Key Features:

• Cloud-based invoicing and expense tools

• Works well with A2X for Amazon sync

• Strong international tax support

Pros:

✔️ Cheaper than QuickBooks

✔️ Great for non-U.S. sellers

Cons:

🚩 Limited customization and U.S. payroll tools

🚩 Still requires A2X or manual effort for Amazon

Pricing:

Starts at $20/month (Starter) to $78/month (Premium)

4. A2X

Best for: Sellers using QuickBooks or Xero who want precise Amazon reconciliation and hands-off syncing.

Key Features:

• Connects Amazon directly to your accounting software

• Breaks down settlements, fees, and reimbursements

• Supports multi-region and multi-SKU data

Pros:

✔️ Incredible accuracy

✔️ Saves hours of manual reconciliation

Cons:

🚩 Must be used with another tool (like QBO/Xero)

🚩 Doesn’t replace a bookkeeper or tax pro

Pricing:

$29/month (Mini) to $199/month (Premium)

Top 5 Inventory Management Software for Amazon FBA

You’ve stocked out for the third time this quarter. Sales plummet, rankings drop, and now you’re rushing to reorder with no real forecast.

The right inventory tool could’ve warned you weeks ago.

Amazon FBA sellers operate on razor-thin margins. Without the right system, stockouts, over-ordering, and missed restocks can quickly eat into profits. 

Here are the top tools built specifically to manage the complexity of FBA inventory.

1. SoStocked

Best for: Forecast-heavy brands with high SKU turnover and complex supply chains

What it does: Custom restock forecasting, lead time padding, seasonal sales modeling, and inventory dashboards

Bonus Value:

• Works well with Xero for accounting, A2X for reconciliation

• Minimizes stockouts and over-ordering with accurate demand forecasting

• Reduces manual spreadsheets with drag-and-drop order planning tools

• Unlocks cash flow visibility by tying inventory to revenue projections

📌 Pairing Suggestion: SoStocked + Xero + A2X = Lean, scalable ops with accurate forecasting

2. Sellerboard

Best for: New or mid-tier sellers focused on profitability and PPC tracking

What it does: Tracks real-time profit by SKU, PPC ROI, refunds, and COGS

Bonus Value:

• Works well with QuickBooks for accounting, doola Bookkeeping for expert oversight

• Highlights unprofitable products before they drain your margins

• Monitors Amazon fees and ad spend in one place; no need for separate dashboards

• Ideal for solo sellers who need clarity, not complexity

📌 Pairing Suggestion: Sellerboard + QuickBooks + doola = Smart starter stack with expert backup

3. InventoryLab

Best for: Retail arbitrage sellers and small private label brands

What it does: Offers product listing, labeling, inventory tracking, and profitability analytics

Bonus Value:

• Works well with A2X for clean bookkeeping, Xero for financial reports

• Streamlines FBA shipments with label printing and box content tools

• Saves time for RA sellers sourcing dozens of SKUs weekly

• Integrates sourcing insights with real-time profit tracking

📌 Pairing Suggestion: InventoryLab + A2X + Xero = From sourcing to P&L, automated

4. SkuVault

Best for: Established sellers with multi-channel or warehouse operations

What it does: Real-time warehouse management, barcode scanning, stock sync, and order fulfillment

Bonus Value:

• Works well with QuickBooks for advanced accounting, doola for tax compliance

• Supports multiple warehouses and sales channels (Amazon, Walmart, Shopify, etc.)

• Improves fulfillment speed and accuracy with barcode-based picking

• Scales with your business as you add new SKUs, teams, or channels

📌 Pairing Suggestion: SkuVault + QuickBooks + doola = Enterprise-level control with expert tax and finance support

Choose the Right FBA Software Stack

When to Use Software? When to Consider Professional Help?

Many Amazon sellers start with DIY tools or plug-and-play software stacks, and that works fine in the beginning. But as your business grows, the cracks start to show.

While software automates the “what,” professionals handle the “why” and “how.”

They don’t just log numbers, they interpret them. They catch patterns, adjust strategies, and make sure you’re compliant with both U.S. tax rules and Amazon’s ever-changing ecosystem.

However, just because a dashboard looks polished doesn’t mean your finances are accurate. Even top-tier software can’t always catch:

• Misclassified expenses that throw off your tax deductions

• Overwritten Amazon-native data that leads to reporting errors

• Improper inventory tracking, which messes with your COGS and margins

This is the illusion of accuracy. The reports look clean, but the logic behind them is off.

And that’s where tax problems start, which require a professional.

If you’re experiencing any of the following, it might be time to bring in professional help:

• You’re selling on multiple marketplaces (Amazon + Walmart, Shopify, etc.)

• You have multi-state sales tax obligations and aren’t sure if you’re compliant

• Ad spend on Amazon PPC is distorting your profitability reports

• You’re seeing reconciliation errors or mismatches every month

• You’re frequently correcting your books or missing transactions

• You’re confused by how refunds, reimbursements, or COGS are recorded

If you check 3 or more, it’s time to upgrade to expert help from doola.

Why Amazon Sellers Use doola Bookkeeping With Their Software Stack

Your accounting software pulls in the numbers.

Amazon sends reports. Inventory tools track stock movement. But who’s connecting the dots? 

A seller spent 6 hours a week manually reconciling Amazon deposits, guessing at ad spend attribution, and filing late taxes due to unclear reporting.

With doola, they got: Automated entries, expert-reviewed books, and full clarity on real profits, all while still using tools like A2X and QuickBooks.

We don’t replace your stack, we optimize it:

✅ Custom Reconciliation: We clean up what automated syncs miss, like mismatched payouts or miscategorized refunds.

✅ Sales Tax, State by State: Selling across borders? We handle the nexus math and prep for every jurisdiction.

✅ Filing Support: From estimated quarterly taxes to year-end returns, we prep, guide, and file.

✅ Profit/Loss Insights: We surface what software can’t, like how ad spend is eating your margins or when to restock your top SKUs.

We work behind the scenes with your tools, and in front of them with expert guidance. So, you get the best of both worlds: automation + strategy.

Hear It From Founders Like You

“doola has been super helpful in handling the legal and financial setup of Flagaholics so we could focus on what mattered—building a brand, refining our products, and delivering a top-tier customer experience.”
        — Adam Fuller, Founder of Flagaholics

Let doola Handle the Hard Parts of Your Amazon FBA Finances

You’re here: Spending hours juggling spreadsheets, wondering if you’re overpaying taxes, missing Amazon reimbursements, or unsure what your actual profit looks like.

We take you here: Accurate books, stress-free tax filings, clean reconciliations, and a clear financial roadmap, backed by real experts who understand Amazon FBA inside out.

With doola Bookkeeping, you get a dedicated partner who keeps your business compliant, tax-ready, and focused on growth.

✅ Sales tax filings? Handled.

✅ Books? Clean and audit-ready.

✅ Profit insights? Delivered.

✅ Time spent guessing? Gone.

Ready to scale without financial guesswork? Let doola take the load off, so you can get back to running your Amazon business.

Sign up today and turn clarity into momentum.