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Bookkeeping Tips For E-Commerce Companies

Running an e-commerce enterprise comes with its own set of unique challenges.  One critical aspect is managing your finances effectively. Accurate bookkeeping/accounting is essential for staying on top of your overall cost structure, tracking inventory and sales, and ensuring compliance with various tax obligations. In this article, we’ll provide you with some valuable bookkeeping tips to help e-commerce companies stay organized and optimize their overall financial health.

1. Separate Your Business and Personal Finances

When you start an e-commerce business, it’s essential to establish separate bank accounts and credit cards exclusively for business transactions. Co-mingling personal and business finances can quickly become a headache to untangle when it comes to bookkeeping. Having separate accounts simplifies tracking income, expenses, and documenting transactions solely related to your business function.

2. Invest in Accounting Software

Investing in accounting software designed for small businesses or e-commerce companies can significantly streamline your bookkeeping processes. Accounting tools like QuickBooks, Xero, or Wave offer features tailored to e-commerce businesses, enabling you to track sales, manage your inventory, and generate customized financial reports efficiently. These tools can also allow you to automate tasks and centralize financial data, saving you time and reducing the risk of potentially costly errors.

3. Regularly Track Sales and Expenses

Constantly monitoring your sales and expenses is vital for accurate bookkeeping. Keep track of all income and expenses related to your e-commerce business, including product costs, packaging materials, shipping costs, marketing and advertising expenses, platform fees, subscriptions, etc. Reviewing and reconciling your financial data on a monthly basis will help identify any discrepancies or potential flags early on.

4. Organize and Categorize Transactions

Properly categorizing your transactions is essential for accurate financial reporting and tax compliance. Set up specific chart of accounts tailored to your e-commerce business, including categories such as sales revenue, cost of goods sold (COGS), advertising expenses, shipping expenses, and platform fees. Regularly assign transactions to the appropriate categories to maintain organized and meaningful financial records.

5. Regularly Track Inventory

If your e-commerce enterprise involves selling physical products, properly managing your inventory function is critical for accurate financial reporting. Implement an inventory management system that integrates seamlessly with your accounting software. If using a POS system like Square, make sure this too syncs well with your chosen accounting software.  This allows you to track inventory levels, calculate the cost of goods sold, and generate inventory and profitability reports easily. Accurate inventory management ensures you have a clear understanding of your profitability by class and helps prevent stockouts or overstocking.

6. Recording Merchant Fees

If your e-commerce store is hosted on one of the major industry platforms like Shopify, you’re already no doubt familiar with the “necessary evil” of merchant processing fees. Make sure not to neglect them when it comes to your bookkeeping efforts as they tend to add up quite significantly over time.  Take them out of net sales and add them to a Bank Deposit along with Gross Sales.  Remember, merchant fees are included in net sales, not in gross sales.

7. Staying on Top of Sales Tax Obligations

E-commerce businesses often have complex sales tax obligations due to selling products to customers in different states or even different countries. Make sure to research and understand the sales tax requirements for each jurisdiction in which you have a nexus or physical presence. Use accounting software or sales tax automation tools to calculate and collect the correct amount of sales tax for each transaction. Timely remittance of sales tax is crucial to avoid penalties and maintain compliance with State and County Tax Authorities.

8. Seek Out Professional Support

Navigating the complexities of e-commerce bookkeeping can be overwhelming, especially as your business really starts to grow. Consider seeking professional assistance from an accountant or bookkeeper experienced in e-commerce or inventory management. They can help set up your accounting system, provide advice for optimizing financial processes, track your inventory, and ensure compliance with various tax regulations. Professional expertise can save you time and give you peace of mind knowing that your finances are in proper order.


Following these bookkeeping tips will help e-commerce businesses streamline their financial management processes and ensure accurate and timely reporting. By separating personal and business finances, utilizing accounting software, tracking sales and expenses, and seeking professional support when needed, you can achieve financial health and focus on growing your e-commerce business. Remember, accurate bookkeeping is not just a necessity for compliance but also a foundation for making informed financial decisions and achieving long-term success.

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