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Managing Shopify Marketplace Connect Channels With Bookkeep

Overview​

Shopify’s Marketplace Connect app allows you to expand your business by selling across multiple marketplaces such as Amazon, Walmart, Target, and eBay—all managed through your Shopify account.

While this is a great way to reach more customers, it also means your sales and payments are combined into a single Shopify dataset. Without proper segmentation, this can make accounting and reporting more complex.

That’s where Bookkeep’s segmentation feature comes in. Segmentation allows you to maintain separate Chart of Accounts mappings for one or more sales channels within Shopify, ensuring accurate and organized financial reporting.

How Bookkeep Handles Shopify Marketplace Connect​

When you connect your Shopify account to Bookkeep, we automatically sync your daily financial summaries—including sales, refunds, fees, and payouts. With Marketplace Connect, these transactions can include data from multiple sales channels such as Amazon, eBay, Target, or Walmart.

One important note: fees and payouts for third-party marketplace orders are not synced into Shopify. We generally recommend relying on the source platform data instead. For example, use Bookkeep’s direct integrations with Walmart, eBay, and Amazon, and exclude these segments from your Shopify connection to prevent duplicate data. This ensures you’re pulling data directly from the source (e.g., Walmart) for complete accuracy.

Using Bookkeep’s segmentation feature, you can:

  • Split each marketplace (Amazon, eBay, Walmart, Target, etc.) into its own segment for a dedicated mapping or exclusion. You may even see Amazon segmented by region—for example, Amazon US and Amazon Canada.

  • Map each channel to a unique Chart of Accounts mapping in your accounting platform (e.g., QuickBooks Online, Xero, or NetSuite).

  • Generate more accurate reports, enabling performance and profitability analysis per marketplace.

  • Exclude channels in your Shopify setup where Bookkeep offers a direct integration (e.g., Walmart, eBay, Amazon) to ensure complete and unduplicated data.

Example​

Suppose your Shopify account sells:

  • Walmart orders via Marketplace Connect and Walmart.com

  • Target orders through Shopify Marketplace Connect

With Bookkeep, you can:

  • Exclude Walmart data from Shopify by turning off the Walmart segment, since you can connect Walmart directly to Bookkeep for more complete data (including fees and payouts).

  • Keep Target as a separate sales channel for better visibility in financial reports (a direct Target integration is not available at this time).

This setup ensures your accounting accurately reflects where sales occur—without duplication.

Benefits of Using Segmentation​

✅ Accurate channel-level reporting – See which marketplaces drive revenue and profit.
✅ Clean data in your accounting system – Avoid double-counting when you connect multiple apps.
✅ Flexible control – Include or exclude channels as your workflow requires.

How to Set Up Segmentation for Shopify Marketplace Connect​

  1. Go to your Shopify connection in Bookkeep.

  2. Under the Shopify connection settings, choose “Segment by Sales Channel.”

  3. Review the list of detected sales channels (e.g., Online Store, Amazon, Walmart, Target, eBay, etc.).

  4. Assign Chart of Accounts mappings for each channel, or group multiple channels into a single segment if desired.

  5. Optionally, disable or exclude any marketplace data (e.g., Walmart) if that marketplace is already connected directly to Bookkeep. Below, I have isolated the Walmart data so that these entries can be turned off, allowing us to rely instead on the direct Walmart integration.

  6. Save your settings — Bookkeep will automatically post segmented Shopify entries going forward.

Best Practices for Multi-Channel Shopify Accounting​

  • If a marketplace (like eBay) is connected both through Shopify and directly in Bookkeep, exclude it from Shopify segmentation to avoid duplicate entries.

  • Regularly review your sales channel breakdowns as you add new marketplaces so you can segment them accurately for reporting and reconciliation.

Summary​

Shopify’s Marketplace Connect simplifies multi-channel selling, and Bookkeep ensures your Shopify accounting remains accurate and organized. Using segmentation, you can achieve channel-level visibility and maintain accurate journal entries, all while avoiding duplication.