Best Accounting Software for Amazon Sellers in 2025

Most Amazon and Amazon FBA sellers rely on accounting software to decipher Amazon’s bi-weekly payouts and settlement reports, which offer little to no information about fees or COGS. 

Even if you master Amazon’s native reports, handling bookkeeping for a high volume of transactions, returns, and chargebacks can become overwhelming. This leaves you struggling to accurately record and reconcile Amazon fees, revenue, loss, and other expenses, leading to inaccurate records, delayed reconciliations, and incomplete financial statements.

If you’re rowing a similar boat, choose a suitable accounting software to automate bookkeeping, stay tax-compliant, and manage inventory well. Here are some of the best accounting software for Amazon FBA and Amazon sellers.

Top features to consider when choosing accounting software for Amazon sellers

When evaluating Amazon accounting software, look for the following features. 

1. Ability to support diverse integrations

Accounting for Amazon requires managing many moving parts. For example, you must stay informed about Amazon’s policies and regulations while maintaining competitive product pricing.

Accounting software that supports various third-party integrations, from CRM platforms to sales tax management tools, will help you build a network of interconnected applications to streamline and automate tedious Amazon operations. This includes data management, inventory tracking, invoicing, and more.

2. Inventory management

Overstocking, understocking, incorrect tracking, refunds, and storage are common inventory challenges when selling on Amazon. But even a little mismanagement can prove costly. 

Here’s one scenario: Imagine you accidentally ship a batch of items with some error. In such a case, Amazon will charge a separate fee to have the batch fixed and re-sent.

This is why accounting software with inventory management features, such as real-time alerts for stock levels and automated inventory and sales data syncing, are often the best options.

3. Expense management

Amazon charges different types of fees from the sellers, including FBA fees, referral fees, monthly subscriptions, refund administration fees, and other relevant expenses. Then, there are the added costs of advertising and inventory purchases.

How do you account for revenue, profit, loss, and expenses across categories? This is particularly important when selling in different currencies or states where the fee levied differs, as there can be tax filing errors and miscalculations of profit margins. 

A suitable Amazon and Amazon FBA accounting software will allow you to integrate with Amazon Seller Central seamlessly. It will automatically import and categorize the sales data from your settlement reports while eliminating manual errors and compliance complications.

4. Financial reporting

Another feature to prioritize is financial reporting. Since Amazon's operations and charges are dynamic, sellers may not always have a holistic picture of their expenses, revenue, and profitability. Moreover, Amazon settlement reports often leave out important details like sales tax collected.

Consider PartyMachines, for instance. Webgility’s insights into individual sales channels helped the company understand its true reach and potential on Amazon, allowing them to make strategic moves and realize 65% of its revenue through Amazon.

Your accounting software should fill such gaps by presenting a single source of truth for all transactions and providing access to real-time insights about every sales channel.

Top accounting software for Amazon sellers: A quick overview

Below is a snapshot of the best Amazon and Amazon FBA accounting software.  

Top accounting software for Amazon sellers: A detailed comparison

Here are four of the best Amazon and Amazon FBA accounting software to consider.

1. QuickBooks Online + Webgility

QuickBooks by Intuit is a go-to choice for Amazon sellers and accountants who are handling their bookkeeping and accounting. This cloud-based solution is widely used for its strong features, including multi-channel inventory management, real-time cash flow tracking, and advanced reporting, suitable for smaller operations and Amazon sellers trying to scale.

While QuickBooks offers its very own Amazon Seller Connector, the integration has earned more negative reviews from customers than positive ones. Webgility is a better alternative to connect your Amazon store with QuickBooks.

What are the benefits of connecting Webgility with QuickBooks?

The Amazon Seller Connector by QuickBooks claims to streamline expense management by directly pulling transactions from Amazon and providing automated financial reports to help you understand profitability.

But many complain that the software only allows you to download a limited number of transactions. The rest must be done manually, which defeats its purpose, and limits the growth of bigger sellers.

On the other hand, Webgility offers the most seamless Amazon to QuickBooks integration, allowing sellers to automatically post Amazon transactions as sales orders, receipts, invoices, or estimates.

You get a summary view of your Amazon settlement reports, with a detailed breakdown of every expense. This helps you accurately differentiate between expenses charged by Amazon and others. Moreover, QuickBooks Online also integrates with software like Square, SOS Inventory, HubSpot, and more, helping you create a highly efficient system to manage your Amazon operations.

Case in point: Bases Loaded, a retailer specializing in softball and baseball equipment, sought Webgility to integrate its sales channels with QuickBooks while struggling to streamline accounting and order processing for its Amazon and other online stores.

By automating data entry, order processing, and inventory syncing with Webgility, the company soon started handling 1000 orders with virtually no manual work, freeing up its team to focus more on marketing and expansion.

A couple of months into use, Bases Loaded doubled its revenue and 21xed its order volume.

Over 20,000 Amazon and ecommerce sellers trust Webgility to save 10 hours per week on manual tasks and sync over 87 million transitions annually. To get similar results, get started with a free trial now.

Key features

• Cash flow monitoring and projection: Get a microscopic view of your money flowing in and out and cash flow projections for the next 90 days
• Inventory management: QuickBooks Online Plus and Advanced users benefit from real-time inventory tracking. With instant alerts, the software prevents stock shortages as well as understocking when the inventory runs low
• Advanced business reporting: Make data-driven decisions with a holistic view of your Amazon operations in a single dashboard, from balance sheets to cash flow statements
• Mobile application: QuickBooks mobile application to process payments, track expenses, upload receipts, and monitor cash flow from anywhere

Pros

• Multi-currency support for international sales and expenses 
• Scales easily for high-volume Amazon operations 
• Bank-grade security to protect sensitive information
• Provide log-in access to your accountants and other colleagues so they can work with data directly
• Over 750 integrations and add-ons enhance its overall functionality

Cons

• It does have a steep learning curve, especially for those unfamiliar with basic accounting principles
• Its subscription costs may be on the pricier end for small businesses

Pricing

QuickBooks provides four different pricing plans depending on your country and currency of use. If you’re based in the US, you can pick from the following plans:

• Simple Start: $35/month
• Essentials: $65/month
• Plus: $99/month
• Advanced: $235/month

Check their pricing page for the most recent pricing.

2. Netsuite + Webgility

Oracle’s NetSuite is fully cloud-based accounting software with comprehensive ERP and CRM capabilities, which lets Amazon sellers manage their entire business lifecycle from a single platform.

This, along with features like real-time inventory tracking, order management, Amazon-specific reporting, and more, makes NetSuite a preferred option for running large-scale Amazon operations.

However, NetSuite doesn’t directly connect with Amazon. You can use Webgility to integrate NetSuite with Amazon for a seamless flow of data.

What are the benefits of connecting Webgility with NetSuite?

Similar to the QuickBooks integrations, NetSuite Webgility integration offers various features to streamline Amazon accounting. It automates product listings, multichannel inventory tracking, order management, and bookkeeping for real-time business management.

What’s more, Webgility provides personalized onboarding and training by ecommerce accounting experts, making software implementation a breeze.

Top features of NetSuite 

• Deep customization: Modify workflows, data structures, and dashboards with customization features available through the SuiteFlex platform. Its point-and-click interface doesn’t require coding knowledge
• Multi-channel inventory management: Monitor inventory levels in real-time across channels and locations to improve fulfillment, forecast demands, and reduce stockouts
• Advanced order management: Streamline the order-to-cash process across sales channels and fulfillment centers by simplifying the management of returns and refunds
• General ledger: Create a central repository of all transactions, from fees to refunds, to maintain the consistency of financial records

Pros

• Automates various accounting functions, including inventory, payments, billing, and tax management
• APIs to enable custom integrations if a standard connector isn’t available
• Supports multichannel and multicurrency operations
• Scalable subscription that grows with your business
• Modular licensing allows customers to pay for features needed

Cons 

• It can be complex and time-consuming to implement
• Subscription costs increase with the business scale
• On-premise and hybrid setups aren’t available

Pricing 

NetSuite’s pricing plans are based on the company's size and are available on request. You also pay a one-time implementation fee for the initial setup.

3. Xero

Xero is another cloud-based accounting software with a wide range of features to track sales, reconcile bank transactions, and simplify financial management for small to medium-sized Amazon operations.

Its multi-currency support and ease of use have made it the best choice for international selling. However, as far as software adoption is concerned, it comes second to the Webgility-QuickBooks Online integration due to its limited capabilities in handling high-volume transactions and complex data. It doesn’t scale well.

Top features of Xero

• Bank feeds and imports: Automatically import bank transactions into Xero from your bank account or 21,000+ financial institutes globally
• Comprehensive accounting reports: Instant, up-to-date accounting reports whenever you need quick information. View balance sheets, profit and loss, cash flow, and other relevant information
• Real-time collaboration: Collaborate with bookkeeper, employees, and accountant in real-time with up-to-data financial data
• Batch payments: Bundle multiple bills into a batch and make one payment transaction for all

Pros

• Mobile app to run Amazon operations on the go
• Round-the-clock online support
• Integrates with 1000+ third-party apps, including Stripe, Dext, Expensify, and more
• User-friendly interface

Cons

• Lacks robust customer support with 48 hours turnaround times for email communication
• Not suitable for bigger operations due to limited inventory management features and slower processing of high-volume transactions 

Pricing

• Early: $20 per month
• Growing: $47 per month
• Established: $80 per month

4. Sage

Sage, or Sage Accounting, is cloud-based accounting software mostly used by small business owners and solopreneurs on Amazon seeking an all-in-one solution at an affordable price point. 

With features like income and expense tracking, real-time inventory management, and invoicing automation, Sage works well for smaller Amazon sellers. But if you’re scaling operations, QuickBooks Online or Xero will provide better inventory and financial management capabilities.  

Top features of Sage

• Automate invoicing and payment tracking: Save time on manual efforts by automating invoice creation and payment tracking
• Inventory management: Track inventory in real-time with automatic updates on stock levels and alerts for low stocks
• Mobile application: Application for iOS and Android to manage Amazon accounting from anywhere
• Multi-currency support: Conduct business globally with support for multi-currency transactions

Pros

• Customizable one-click and pre-templated reports
• Cloud-connected flexibility and remote data access
• Ability to invite your accountant or colleague to collaborate securely
• Sage marketplace to extend capabilities with a variety of cloud-native apps
• Automatic categorization and recording of receipts

Cons

• Higher pricing compared to competitors for entry-level packages
• Limited third-party integrations

Pricing

• Pro Accounting: $625/year
• Premium Accounting: $1043/year
• Quantum Accounting: $1780/year

Check their pricing page for the latest pricing.

Webgility: The right accounting software for Amazon sellers

Amazon sellers love the Webgility-QuickBooks integration for its ease of use and the personal onboarding support offered through ecommerce experts.

Here are a couple more reasons why 20,000+ Amazon and ecommerce sellers trust Webgility: 

• Automate accounting: Capture, record, and categorize transactions automatically as invoices, sales orders, etc.
• Reconcile settlement reports: Get a clearer view of expenses and fees charged by Amazon versus order related expenses
• Real-time inventory sync: Instantly track, sync, and update inventory quantities and prices
• In-depth analytics: Generate financial reports with growth insights in real-time
• Unlimited users: Every plan supports unlimited users

All of the above saves 70% of Webgility customers up to 10 hours per week on manual processes, improving operations and saving costs.

You can learn more about the integration here. Or take Webgility for a spin here.