Selling products on both Amazon and Shopify is a great way to reach more customers and grow your ecommerce business. Amazon gives you access to an established marketplace, while Shopify allows you to build your own online store and connect directly with customers.
However, managing accounting across both platforms can quickly become complicated.
Each platform has different payment schedules, transaction fees, refund processes, and reporting systems. Without a proper accounting process, tracking your actual revenue, expenses, and profits can become challenging.
The good news? You don’t need to manage everything manually. With the right processes and ecommerce accounting software, you can keep your financial records organized and make better business decisions.
Let’s explore how to simplify accounting when selling on Amazon and Shopify together.
1. Understand the Accounting Differences Between Amazon and Shopify
Although both platforms help you sell products online, they handle transactions differently.
Amazon Accounting
Amazon typically deducts several fees before transferring your earnings to your bank account. These may include:
- Referral fees
- Fulfillment by Amazon (FBA) fees
- Storage fees
- Advertising expenses
- Refunds and other adjustments
As a result, the amount deposited into your bank account is usually lower than your total sales revenue.
Shopify Accounting
Shopify gives you greater control over your online store, but you still need to account for:
- Payment processing fees
- Shopify subscription charges
- Third-party app expenses
- Shipping and fulfillment costs
- Refunds and discounts
Understanding these differences helps you record transactions accurately and avoid financial discrepancies.
2. Keep Your Sales Data in One Place
One of the biggest challenges of selling on multiple platforms is managing separate sales reports.
Amazon provides transaction and settlement reports, while Shopify offers its own sales and payment reports. Switching between these dashboards to calculate total revenue can be time-consuming.
Instead, consider bringing your sales data into one accounting system.
A centralized system helps you:
- Track revenue from Amazon and Shopify separately.
- Monitor overall business performance.
- Identify your best-performing sales channel.
- Reduce manual data entry and accounting errors.
- Generate financial reports more easily.
Using ecommerce accounting software that integrates with both platforms can simplify this process by automatically transferring relevant transaction data into your accounting system.
3. Reconcile Payments and Bank Deposits Regularly
Imagine making $10,000 in Amazon sales but receiving only $8,200 in your bank account.
Where did the remaining $1,800 go?
It may have been deducted for marketplace fees, advertising, refunds, or other adjustments. Without proper reconciliation, these deductions can create confusion.
Bank reconciliation helps ensure your recorded transactions match the money entering and leaving your accounts.
Follow these simple steps:
- Download your Amazon settlement and Shopify payout reports.
- Compare gross sales against refunds, fees, and adjustments.
- Match net payouts with your bank deposits.
- Investigate any missing or unmatched transactions.
- Record differences before closing your books.
Performing reconciliation regularly helps prevent small accounting mistakes from becoming bigger financial problems.
4. Track Inventory Across Both Sales Channels
Inventory management becomes more complicated when you sell the same products through Amazon and Shopify.
For example, if you have 50 units available and sell 20 through Amazon, your Shopify inventory should reflect the updated stock availability.
Without proper inventory synchronization, you risk overselling products or maintaining inaccurate inventory records.
To avoid these problems:
- Use a centralized inventory management system.
- Synchronize stock quantities across both platforms.
- Track the cost of goods sold (COGS).
- Account for damaged, returned, or missing products.
- Review inventory valuation regularly.
Accurate inventory tracking also helps you understand product profitability and maintain reliable financial statements.
5. Manage Sales Tax and Other Tax Obligations
Selling through multiple ecommerce channels can make tax compliance more complex, especially when customers are located in different states or countries.
Amazon may collect and remit certain marketplace taxes on your behalf, while Shopify tax responsibilities depend on your business location, customer location, and applicable regulations.
It’s important to understand which taxes are collected automatically and which remain your responsibility.
Here are a few accounting practices to follow:
- Track taxable and non-taxable sales.
- Identify where your business has tax obligations.
- Separate collected taxes from actual revenue.
- Review marketplace tax collection reports.
- Maintain accurate records for tax filing.
Consulting a qualified tax professional can help ensure your business meets its specific compliance requirements.
6. Monitor Your Expenses and Profit Margins
High sales numbers don’t always mean high profits.
When selling on Amazon and Shopify, expenses can vary significantly between platforms. Amazon may involve marketplace and fulfillment fees, while Shopify may require additional spending on marketing, apps, and payment processing.
Tracking these expenses separately helps you understand which channel generates better returns.
Pay attention to:
- Product purchasing and manufacturing costs
- Marketplace and transaction fees
- Shipping and fulfillment expenses
- Advertising and marketing costs
- Software subscriptions
- Returns and refunds
Calculate profitability for each sales channel rather than relying only on total revenue.
This allows you to adjust pricing, control expenses, and focus on products that contribute the most to your bottom line.
7. Automate Accounting with the Right Software
Manually downloading reports, entering transactions, and matching payouts may work when you’re processing a few orders.
But as your business grows, these tasks become increasingly difficult to manage.
This is where ecommerce accounting software can make a difference.
The right solution can help you:
- Automatically sync Amazon and Shopify sales data.
- Record marketplace fees, refunds, and other deductions.
- Connect sales transactions with accounting platforms.
- Simplify payment reconciliation.
- Reduce repetitive manual accounting work.
- Maintain more accurate financial records.
For example, solutions like Webgility help connect ecommerce sales channels with accounting systems such as QuickBooks, making it easier to manage financial information across multiple platforms.
Automation not only saves time but also allows you to focus more on growing your business.
8. Review Your Financial Reports Every Month
Even with automated accounting, reviewing your financial performance regularly is essential.
Set aside time each month to review:
- Profit and loss statement: Understand your revenue, expenses, and profitability.
- Balance sheet: Monitor your assets, liabilities, and overall financial position.
- Cash flow statement: Track how money moves in and out of your business.
- Sales channel performance: Compare Amazon and Shopify revenue and expenses.
Regular financial reviews help you identify problems early and make informed decisions about inventory, pricing, and business growth.
Final Thoughts
Managing accounting when selling on Amazon and Shopify together doesn’t have to be overwhelming.
The key is to keep your sales data organized, reconcile payments regularly, track inventory accurately, and understand the expenses associated with each platform.
As your order volume increases, investing in reliable ecommerce accounting software can help eliminate manual work and improve financial visibility.
With a streamlined accounting process, you’ll spend less time managing spreadsheets and more time building a profitable ecommerce business.