Finding the Right Amazon Accountants for Your Growing Business

Most general accountants look at your Amazon reports and guess. They categorize fees incorrectly, miss reimbursement opportunities, and deliver financials that do not reflect reality.

The wrong accountant costs you more than their fee in missed deductions and tax surprises. The right one understands marketplace complexity and keeps your books clean.

In this guide, you will learn what separates Amazon accountants from generalists, which questions to ask before hiring, and how to evaluate whether your current accountant actually understands your business.

Why generic accountants fail Amazon sellers

Amazon’s seller accounting complexity outpaces what most generalists can handle. Relying on a standard CPA or DIY approach leads to missed reimbursements, unreliable financials, and costly compliance gaps.

What makes Amazon accounting different?

Amazon settlements contain an average of 15+ fee types that impact your true margins. These include referral fees, FBA fulfillment fees, storage charges, shipping, returns, and more. 

Unlike traditional retail, Amazon nets these fees against your payouts, making it difficult to see your real revenue and expenses without specialized reconciliation.

Table 1: Standard accounting vs. Amazon-specific accounting

The hidden risks of generic accounting

• Missed deductions: Failing to break out Amazon fees means you overstate income and overpay taxes
• Inventory confusion: Without channel-level tracking, you cannot see true margins or prevent stockouts
• Sales tax exposure: Multi-state FBA storage creates a nexus in dozens of states. Generic accountants often miss these triggers, risking audits and penalties
• Manual reconciliation overload: Sellers spend hours monthly pulling reports and matching transactions; time that could be automated

Automation platforms like Webgility handle routine Amazon reconciliation, freeing your accountant to focus on strategy.

Once you hit these triggers, what kind of specialist do you need?

Why the best Amazon accountants use automation (and which tools)

Ecommerce automation is no longer optional for accounting. Here is how it helps Amazon accountants work faster.

Automation platforms like Webgility sync orders, fees, payouts, and inventory in real time. This means your accounting is always up to date, and your accountant can focus on analysis.

Must-have automation features

• Payout reconciliation that matches every order, fee, and refund to your accounting system
• Inventory sync across Amazon and other channels
• Fee mapping for all Amazon settlement types

So, which Amazon accountant types are best equipped to leverage these accounting automation tools?

Mapping Amazon accountant types to your business model

Choose an Amazon accountant based on your business’s stage and needs.

• Bookkeeper: Focuses on transactional, best for under $500K, handles basic reconciliation and reporting
• Tax-focused CPA: Handles compliance, multi-state/international tax, best for $500K–$1.5M
• Tech-enabled accountant: Combines bookkeeping, tax, and automation expertise; ideal for fast-growing, multi-channel sellers
• Fractional CFO/advisory: Provides strategic planning and forecasting, best for $1M+

If you are at $2M, selling FBA and FBM, you need a tech-enabled accountant who can reconcile both fulfillment models, track inventory across channels, and provide monthly margin analysis. Budget $2,000-$4,000 per month for this level of support.

Tech-enabled Amazon accountants often recommend or use Webgility for real-time insights.

Once you know which type you need, how do you vet the right fit?

How to evaluate and hire the right Amazon accountant

A few targeted questions can reveal whether a candidate is the right fit for your business.

Checklist for vetting Amazon accountants

• At least 3 years of direct Amazon seller experience
• Can explain FBA fees, settlement timing, and reconciliation
• Uses or recommends automation (e.g., Webgility)
• Multi-channel experience (Amazon, Shopify, eBay, etc.)
• Clear fee structure and engagement model
• Testimonials from similar sellers

Discovery call questions:

• How do you handle Amazon settlement reconciliation: manually or with automation?
• What is your communication cadence and reporting schedule?
• Have you worked with sellers in my category or revenue range?
• What ecommerce accounting software and integrations do you support?
• Can you provide references or case studies from Amazon sellers?

Red flags to watch for:

• “I do everything in Excel”
• No automation or resistance to using it
• No Amazon clients or relevant case studies
• Unclear or inconsistent pricing

As your business grows, your accounting needs and your accountant’s role will evolve.

From bookkeeper to CFO: When to level up your accounting support

Growth brings new accounting challenges. Here is how to keep up.

Triggers for upgrading your accounting support

• Hitting revenue milestones ($500K, $1M, $5M)
• Expanding to multiple channels or international markets
• Facing inventory and cash flow complexity

How automation and expertise work together

Automation frees up accountants for forecasting, margin analysis, and strategic advisory. This partnership delivers real-time insights and margin growth.

Cost comparison:

Table 1: Cost comparison for Amazon accountants

Timeline: Expect 30-60 days to find, vet, and onboard a specialist Amazon accountant. Complex businesses may take longer.

Webgility bridges the gap between automation and accounting expertise. The platform syncs Amazon orders, fees, settlements, and refunds directly to QuickBooks in real time, eliminating the manual data entry that eats into your accountant's hours.

Your accountant receives clean, categorized data instead of messy exports that require hours of sorting. Fee mapping happens automatically, settlement reconciliation runs without manual matching, and SKU-level profitability is visible without spreadsheet gymnastics.

Danwidth, an accounting consultant, uses Webgility to help his ecommerce clients save an average of 38 hours per month on reconciliation and data entry. His clients collectively saved nearly 1,000 hours of busywork in the first few months and gained visibility into gross profit and fee breakdowns across channels.

Book a demo with Webgility today.

Frequently asked questions (FAQs)

What are the biggest accounting challenges for Amazon sellers?

Most sellers struggle with complex fee structures, multi-state tax rules, and time-consuming reconciliation. Manual processes often lead to errors and missed deductions, so automation and Amazon-specific expertise are crucial.

How much does an Amazon accountant typically cost?

Bookkeepers usually charge $500-$2,000 per month, while tech-enabled accountants range from $2,000-$4,000 per month. Fractional CFOs may cost $3,000-$10,000+ monthly. Costs depend on your business size and complexity.

Why do Amazon sellers need automation in accounting?

Automation saves time, reduces errors, and ensures accurate reconciliation of Amazon’s complex settlements. Sellers using automation platforms like Webgility save up to 90% of reconciliation time and close books 3x faster.

Can one accountant handle both my bookkeeping and taxes for Amazon?

Many modern Amazon accountants offer both services, especially those specializing in ecommerce. This integrated approach improves communication and accuracy, but some sellers prefer separate providers for bookkeeping and tax strategy.