Digital illustration of e-commerce automation, featuring Shopify, QuickBooks Online, A2X, and Finale integration for automating COGS accounting.

Automating Cost of Goods Sold (COGS) in Ecommerce Accounting

Cost of Goods Sold (COGS) is a key metric for e-commerce sellers. It directly affects profitability and financial reporting. Automating Cost of Goods Sold accounting can make the process more efficient and accurate.
 
Automating this process involves connecting e-commerce platforms, inventory management systems, and accounting software to streamline data flow.
 

Instead of manually calculating COGS, automation tools track real-time inventory changes, purchase costs, and sales transactions to generate accurate financial reports. 
 
For e-commerce sellers, COGS tracking is essential for:
 
  • Accurate Profitability Analysis: Knowing the true cost of sold products helps sellers determine profit margins.
  • Tax Compliance: Properly recorded COGS ensures correct tax deductions and accurate profit reporting.
  • Cash Flow Management: Understanding costs helps manage cash flow efficiently and make informed purchasing decisions.
  • Scalability: Automating COGS allows to scale without adding accounting complexity.

Inventory Integration Tools

Several tools help automate COGS accounting for e-commerce businesses. Here we’ll take three commonly preferred tools as examples for Shopify business.
 
A2X
 
A2X connects e-commerce platforms like Shopify and Amazon to QuickBooks Online. It automates revenue and expense reconciliation, including COGS calculations.
 
Finale Inventory
 
Finale is an advanced inventory management system that tracks inventory levels, purchase costs, and stock movements, ensuring accurate COGS reporting.
 
QuickBooks Online
 
QuickBooks Online serves as the central accounting hub, integrating with A2X and Finale to generate real-time financial reports and ensure compliance.
 

Syncing Shopify Sales with QuickBooks Online using A2X

When you sync Shopify with QuickBooks Online, the integration records key transaction details, such as:

  • Revenue – Sales income from products sold.
  • Taxes – Sales tax collected based on customer location.
  • Payment Fees – Fees deducted by payment gateways like Shopify Payments, PayPal, or Stripe.
  • Refunds & Discounts – Returns and promotions are accurately reflected.

The integration reduces manual data entry and ensures that all transactions in Shopify are recorded in QuickBooks Online, providing accurate financial statements.

Article: Managing Ecommerce Accounting with QuickBooks Online

A2X app acts as a bridge between Shopify and QuickBooks Online. It optimizes the way sales data is recorded.

Instead of importing individual transactions, A2X creates summarized journal entries that group sales data into structured financial reports.

Cost of Goods Sold (COGS) in A2X

First of all, you have to enable COGS feature in A2X. When enabled, it automates COGS calculations by pulling inventory costs from connected platforms, eliminating manual tracking errors. 

Once COGS tracking is enabled in A2X, you must assign the appropriate Chart of Accounts in QuickBooks Online:

  • COGS Account – This should match your existing account in QuickBooks, typically labeled as “Cost of Goods Sold.” It records the cost of inventory sold during a given period.
  • Inventory Asset Account – Used to track inventory value on the balance sheet before it is sold. This is often named “Inventory Asset” in QuickBooks.

A2X will pull cost data from your inventory system (such as Finale Inventory) or from manually uploaded cost values.

To avoid discrepancies, verify that A2X correctly maps COGS transactions to QuickBooks:

  1. Go to A2X Settings → Navigate to the COGS Settings tab.
  2. Select the Right Accounts → Assign the correct COGS and inventory asset accounts from QuickBooks.
  3. Check COGS Calculation Method → A2X can use FIFO (First-In-First-Out) or an average cost method, depending on your inventory tracking setup.
  4. Review Sample Entries → Before finalizing, review sample journal entries in QuickBooks to ensure proper categorization.

Handling SKUs and COGS Data with Finale

A2X efficiently syncs Shopify sales data to QuickBooks Online, categorizing transactions by SKU (Stock Keeping Unit). However, while A2X identifies which products were sold, it does not store or update cost details.

This creates a gap in tracking COGS (Cost of Goods Sold), requiring an additional solution to supply accurate cost data.

Article: Key Tasks for Sales and Customers in QuickBooks Online

Without an automated cost-tracking system, e-commerce stores often resort to manual SKU cost updates, which come with several challenges:

  • Entering cost data manually for hundreds or thousands of SKUs can lead to discrepancies.
  • Costs fluctuate due to supplier pricing, currency changes, and bulk purchase discounts. Manual updates don’t reflect these changes instantly.
  • If COGS data isn’t updated promptly, profit margins and financial reports may be inaccurate.

Automating SKU Cost Updates with Finale’s Daily Sync

Finale Inventory integrates with A2X to automate COGS tracking by syncing SKU costs daily.

Here’s how it works:

  1. Every inventory item in Finale has a recorded cost based on purchasing history or predefined values.
  2. Finale pushes updated SKU cost data to A2X automatically.
  3. When transactions are posted to QuickBooks Online, A2X assigns the latest cost values to calculate accurate COGS.

These are the key benefits of using Finale for SKU cost management

Accurate COGS Reporting – Reflects real-time cost changes in financial statements.
No Manual Data Entry – Eliminates the need to update costs manually in QuickBooks or A2X.
Scalability – Ideal for e-commerce businesses handling high SKU volumes with frequent pricing updates.

Finalizing Cost Data in A2X

Once Finale has synced SKU costs, the final step is to ensure that A2X correctly applies the latest cost data before it is pushed to QuickBooks Online.

This process involves refreshing, reviewing, and adjusting COGS data when necessary to maintain accuracy.

After Finale completes its daily cost sync, A2X must be refreshed to apply the updated cost data:

  1. Log into A2X and navigate to the COGS settings.
  2. Click Refresh Cost Data to pull the most recent SKU costs from Finale.
  3. A2X automatically updates COGS calculations for all sales transactions.

After this, every order reflects the most up-to-date product costs. It improves the accuracy of profit margins and financial reports.

Viewing Updated COGS Calculations in A2X

You can review the COGS calculations in A2X:

  • Go to the Transactions tab in A2X.
  • Select a recent sales entry and expand the details.
  • A2X will display COGS values calculated using the newly imported SKU costs from Finale.
  • Review the COGS totals before approving the transaction for export to QuickBooks Online.

Overriding or Adjusting Costs When Necessary

Although A2X automatically applies the latest cost values, there may be situations where manual cost adjustments are needed:

  • Supplier price changes not yet reflected in Finale – If Finale has outdated cost data, you can override the cost in A2X for specific transactions.
  • One-time adjustments – If a particular sale involves a discounted or bulk purchase cost, you may need to manually adjust the COGS in A2X before exporting the data to QuickBooks.
  • Error correction – If cost discrepancies appear, you can manually edit the cost per SKU before finalizing the sales entry.

Syncing COGS Data with QuickBooks Online

The final step in automating Cost of Goods Sold (COGS) accounting is ensuring that A2X accurately posts COGS entries into QuickBooks Online (QBO). It ensures that inventory costs are properly recorded in financial statements, providing clear insights into profitability.

Once A2X finalizes the COGS calculations, the system automatically syncs these entries to QuickBooks Online.

The process follows these steps:

  1. Review transactions in A2X – Ensure the correct COGS values are assigned before exporting.
  2. Export transactions to QuickBooks – A2X posts summarized COGS journal entries to QuickBooks Online.
  3. Verify entries in QuickBooks – Check the posted journal entries to confirm accuracy.

Such seamless integration eliminates the need for manual COGS adjustments, reducing errors and saving time.

The Journal Entry Structure

When A2X exports COGS data to QuickBooks, it creates a journal entry that reflects the movement of inventory costs.

The standard accounting entry follows this format:

COGS Account (Debited) – The cost of sold products is recorded as an expense.
Inventory Asset Account (Credited) – The inventory balance is reduced based on the cost of goods sold.

Example Journal Entry:

DateAccountDebit ($)Credit ($)
03/08/2025Cost of Goods Sold5,000
03/08/2025Inventory Asset5,000

This entry ensures that inventory decreases as products are sold, while COGS accurately reflects business expenses.

Viewing Updates in Financial Reports

Once the COGS data is posted in QuickBooks Online, the impact can be observed in key financial statements:

Profit & Loss Statement (P&L) – The COGS amount is reflected under expenses, directly affecting gross profit.
Balance Sheet – The inventory account decreases, showing the reduction in available stock.
COGS Detail Report – A2X provides a breakdown of COGS calculations, allowing business owners to track costs by SKU, date, or order.

Conclusion: Automating Cost of Goods Sold (COGS) in Ecommerce Accounting

For e-commerce businesses, automating the accounting of the Cost of Goods Sold (COGS) is important. It helps maintain accurate financial records and gives clear insights into profitability.
 
Using A2X, Finale Inventory, and QuickBooks Online together, allows e-commerce sellers to make COGS tracking easier, more accurate, and in line with best accounting practices.
 
A2X syncs sales data from Shopify, Finale updates SKU costs automatically, and QuickBooks Online records all the financial entries. This creates a smooth, complete system for tracking COGS.
 
With it, e-commerce businesses can accurately track their costs, manage inventory better, and create reliable financial reports to make smart decisions.
 
Using these automation tools, e-commerce owners save time, improve accuracy, and get real-time financial insights.
 
This lets them focus on growing their business efficiently.
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