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Mastering Amazon Bookkeeping: A Complete Guide for Sellers
Author: E2E Accounting Team
Date: May 14, 2025
Category: eCommerce
Views: 13 views

As an Amazon seller, financial management is much more than just keeping track of sales. Accurate and up-to-date bookkeeping is vital for long-term profitability because of the numerous income sources, frequent transactions, intricate Amazon fee structures, inventory movement, and tax compliance requirements.

Amazon sellers of all experience levels, whether you have just started or are managing a well-established online store. Everyone will be able to comprehend and use sound bookkeeping procedures. This guide will teach you how to properly record sales and refunds, handle Amazon’s various fees (such as FBA, referral, and storage fees), reconcile settlements with your bank accounts, and adhere to regional sales tax or VAT regulations.

Additionally, we will discuss how to get ready for tax season, what data to frequently check to evaluate the financial health of your store, and tools and software that can help automate some of the process. By using the proper bookkeeping technique, you can improve your understanding of your cash flow, profit margins, and overall performance, in addition to avoiding expensive errors and penalties.

Why Amazon Bookkeeping Matters?

One of the most important aspects of selling on Amazon is Amazon bookkeeping, even if it may not be the most fun. For sellers using Fulfillment by Amazon (FBA), maintaining accurate and current financial records is crucial to staying profitable, compliant, and in control of Amazon’s complex ecosystem.

  • Hidden Costs and Complex Fees: A variety of fees that Amazon sellers must deal with can quickly reduce their earnings if they are not carefully tracked. The size, weight, and length of time a product is kept in storage affect the FBA fees, including storage, fulfillment, and removal costs. Furthermore, without effective tracking of expenses and clear planning, Pay-Per-Click (PPC) advertising expenditures can rise, making it challenging to determine the true return on ad spend.
  • Cash Flow Challenges: Payout delays are another problem. Usually, Amazon releases seller payments every 7–14 days, so you frequently have to pay for advertising, inventory, and other costs before you get paid for your sales. Inadequate bookkeeping might result in missing opportunities, cash flow problems, or even excessive spending.
  • VAT Compliance in the UK: Compliance with Value Added Tax (VAT) is of the highest priority for sellers in the UK. Tracking taxable sales, collecting the appropriate amount of VAT, and timely filing of accurate returns are important whether you are VAT registered willingly or because of the threshold. Another layer of complexity that effective bookkeeping helps handle is added by cross-border sales and evolving VAT regulations, particularly in the wake of Brexit.

The Benefits of Good Bookkeeping:

  • Clear Profitability: Recognise your actual profit margins after deducting marketing expenses, taxes, and fees.
  • Better Decision-Making: Use precise Amazon bookkeeping data for pricing, stock planning, and advertising.
  • Tax readiness: Maintain well-organised records to help you be ready for HMRC filings, audits, and VAT returns.
  • Improved Cash Flow Management: Having a thorough understanding of your money allows you to effectively plan your spending.
  • Scalability: Create a solid financial base to sustain investor confidence and business expansion.

eCommerce Bookkeeping vs. Amazon Bookkeeping: Key Differences

AspecteCommerce BookkeepingAmazon Bookkeeping
Platform FeesUsually restricted to platform commissions (like Shopify and Etsy) and payment gateway fees (like Stripe and PayPal).includes several levels: storage costs, FBA fulfillment fees, referral fees, return and refund fees.
Sales ReportingPayouts are easier to match when they are clear and arranged by order.Complex settlement reports that include refunds, adjustments, fees, and sales into a single payout.
Payout TimingThrough gateways, payments are frequently received promptly or in 1-2 days.Amazon requires precise accruals and cash flow forecasting because it pays out every 7–14 days.
VAT / Tax complianceDepending on the area, sellers are directly in charge of either sales tax or VAT.In some cases, Amazon auto-collects VAT. Sellers are still in charge of accurately recording, submitting, and classifying VAT.
Refunds & ReturnseCommerce bookkeeping is usually simple, managed, and documented by the seller.Amazon applies Refunds and fees promptly, necessitating a thorough breakdown of books.

Getting Started with Amazon Bookkeeping: A Step-by-Step Plan for Overwhelmed Sellers

  • Understand why Bookkeeping Matters: The financial foundation of your Amazon business is bookkeeping. You may use it to monitor your actual profitability, stay in compliance with tax laws, and make well-informed decisions based on facts rather than guesswork.
  • Choose a Bookkeeping Method: Choose between accrual and cash accounting. Accrual accounting is straightforward and only records transactions when money enters or exits your account. Whereas, cash accounting recognises revenue when cash is received and when expenses are paid.
  • Set Up a Business Bank Account: Create a distinct bank account that is only used for business purposes. This makes keeping records easier and guarantees that personal and business finances are clear, which is important for tax preparation and audits.
  • Choose Your Tools: Choose between investing in accounting software or using a manual approach, such as spreadsheets. Many of the processes may be automated with tools like QuickBooks, Xero, or Amazon-integrated programs like A2X, which can grow with your company.
  • Track Your Income: To accurately record gross sales, refunds, fees, and the final payout to your account, you must examine records such as Settlement Statements. Amazon pays you net of fees and other deductions.
  • Record Your Expenses: Keep thorough records of all business-related expenditures, such as product costs, advertising expenditures, software subscriptions, Amazon fees, and packing materials. Maintaining records of every transaction is necessary for tax deductions and audits.
  • Track Inventory: One important financial statistic is that the cost of goods sold (COGS) is directly impacted by inventory. Keep track of your sales, purchases, units on hand, and inventory valuation, particularly if you’re using FBA.
  • Set a Bookkeeping Schedule: Consistency is key. Schedule a weekly or biweekly bookkeeping session to track revenue and expenses, reconcile bank accounts, and verify inventory levels. This helps prevent backlogs and keeps your finances under control.
  • Review Financial Reports Monthly: Regularly review your cash flow statement, balance sheet, and profit and loss statement. These reports provide information on how well your company is doing and point out areas that could use improvement or cost reduction.

Common Amazon Bookkeeping Mistakes and How to Avoid Them

The number of errors may be more or less, depending on the accounting procedures and expertise used by a business to keep its financial records up to date.

Irregular Recording of Transaction Recording:

Financial statements become inconsistent when transactions are not immediately recorded or when information is not logged consistently. This problem is more common in small organisations that use manual processes.

This will result in issues such as mismatches during bank reconciliations, inaccurate profit and loss computations, and errors in cash flow management.

How to avoid this?

  1. Automate transaction entries: To guarantee that transactions are documented as soon as they happen, purchase accounting software such as Tally.
  2. Create a routine: To maintain up-to-date financial records, make it a habit to update the books of accounts every day or every week.
  3. Assign Responsibility: Make sure that a team member is in charge of accurately and promptly documenting transactions.

Wrong Classification of Expenses and Income:

Financial statements can be affected when transactions are misclassified, such as when a capital expense is mistakenly classified as a routine business expense. Businesses that are not familiar with accounting standards often make this mistake. These errors result in false financial reports, inaccurate tax computations, and even legal issues.

How to avoid this?

  • Understand the fundamentals of accounting: To prevent mislabeling, business managers should be aware of the basic classifications of income and expenses.
  • Utilise established software categories: The majority of contemporary accounting software has predefined categories designed specifically for companies. Utilise them to reduce mistakes.
  • Perform recurring evaluations: Cross-check your books with an auditor or financial expert to identify and fix any misclassifications early.

Neglecting to Maintain Receipts and Invoices:

Verifying transactions requires accurate documentation, particularly when it comes to tax audits. But a lot of companies don’t maintain proper records, especially when it comes to small cash transactions. It will lead to issues with the inability to provide evidence of expenses during tax investigation, a higher chance of tax claims being denied, and the loss of the GST input tax credit (ITC).

How to avoid this?

  • Digitisation of records: Save digital copies of all invoices and receipts using mobile applications or scanners so they are available when needed.
  • Adaptation of a structured filing system: To make retrieval easy and effective, group receipts by date, vendor, and purpose, whether they are digital or physical.
  • Plan a frequent review: Make time each week to go through and submit receipts to ensure that no transaction is overlooked.

Mixing Personal and Business Expenses:

Mixing personal and business transactions is the most frequent error, at least for small business owners and sole proprietors. Reconciliation is complicated, for instance, when personal purchases are made using the corporate account and vice versa. Missed financial reporting, trouble estimating precise tax obligations, and issues during audits are the outcomes.

How to avoid this?

  • Creating distinct bank accounts: Keeping personal and corporate accounts distinct helps prevent confusion when it comes time to file taxes.
  • Using technological tools: Make use of accounting apps and financial software that automatically classify transactions based on account type to reduce human mistakes.
  • Establish clear boundaries: Clearly explain to all parties involved, including family members and staff, the importance of maintaining distinct financial practices for personal and professional purposes.

Ignoring the Bank Reconciliation:

Bank reconciliation is the process of comparing bank statements and the company’s financial records to make sure they match. Since they believe it is unnecessary, many small firms omit this step. The problem is caused by several factors, such as failing to notice fraudulent transactions or bank problems, inconsistencies in cash flow records, and trouble following up on returned checks or processing payments.

How to avoid this?

  • Conduct monthly reconciliations: Arrange for a routine examination to compare bank statements and transactions in your records to spot inconsistencies.
  • Make use of technology: A lot of accounting software programs come with integrated bank reconciliation features that can identify discrepancies in entries automatically.

Amazon Bookkeeping Software: Your Key to Simplified Finances

  • QuickBooks Commerce: Controls inventory, automates spending, and synchronizes Amazon sales.
  • Xero: Simple bank reconciliation and third-party app integration with Amazon.
  • A2X Accounting: Amazon sellers are the target audience for A2X Accounting, which automatically classifies payouts.
  • GoDaddy Online Bookkeeping: Simple income and tax tracking solution for small Amazon enterprises.
  • Zoho Books: Excellent for Amazon sellers with multiple channels; manages payments, invoicing, and reports.

Amazon FBA Accountants: Expert Help for Complex Finances

It might be challenging to manage your money as an Amazon FBA seller. eCommerce-focused FBA accountants assist with inventory management, profit analysis, and tax compliance. Their knowledge guarantees accurate records and wiser financial choices, allowing you to concentrate on expanding your company.

Why Choose E2E Accounting?

We at E2E Accounting offer complete, end-to-end financial solutions that are intended to streamline your business processes and foster expansion, so that you can concentrate on what matters- managing your business. Our team of expert eCommerce accountants provides a wide range of services, including amazon bookkeeping, payroll, tax preparation, compliance, and strategic advising.

We provide precise, real-time insights that help people make better decisions by integrating the newest technology with extensive industry experience. Our scalable and customised strategy guarantees that you get the appropriate amount of support at every stage, regardless of your business size.

Conclusion

The foundation of any successful Amazon business is sound bookkeeping. Understanding your financial flow, controlling inventories, getting ready for taxes, and making wise judgments are all more important than simply keeping track of numbers.

Smart Amazon bookkeeping software and reliable eCommerce accountants can assist sellers in streamlining complicated financial procedures so they can concentrate on expansion. Learning your bookkeeping can help you stay ahead of the game, whether you’re managing FBA fees, balancing paychecks, or making expansion plans. Invest in the appropriate equipment and professional advice to create a prosperous and long-lasting business.


E2E Accounting Team

The E2E Accounting team combines expert accountants, legal specialists, and industry advisors to provide valuable insights into finance and compliance. With hands-on experience, we create content that informs, educates, and empowers business owners. From financial strategies to legal updates, our content serves as a reliable guide, ensuring accuracy, clarity, and a deep understanding of business challenges.

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