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Syncing Inventory Costs from Shopify POS to QuickBooks in a Multi-Store Setup

This article helps Webgility Desktop users how to correctly configure the synchronization of inventory cost data from Shopify POS to QuickBooks Desktop Enterprise, particularly in setups involving multiple Shopify stores. It emphasizes the importance of proper configuration to ensure accurate Cost of Goods Sold (COGS) reporting and prevent data inconsistencies.

Overview

This guide explains how to correctly configure the sync of inventory cost data from Shopify POS to QuickBooks, especially in environments with multiple Shopify stores. Proper setup is critical to maintain accurate Cost of Goods Sold (COGS) reporting and avoid data inconsistencies.

Key Considerations
Master Store Sync: Only one Shopify store should be designated as the master data source for cost data.

Sync Conflicts: Syncing cost data from multiple stores can result in discrepancies and inaccurate COGS in QuickBooks.

Manual Adjustments: Non-master stores should not sync cost data automatically. Cost entries from these stores must be managed manually in QuickBooks.

Step-by-Step Configuration
1. Access Sync Settings
Log into your Webgility Product then Go to Settings > Data Sync > Inventory/COGS Sync.

2. Configure the Master Store
Identify the primary Shopify store with the most reliable cost data.

Select this store and enable “Store as Master Data” in the sync settings.

Ensure the direction of sync is from Shopify to QuickBooks (not the other way around).

Save the configuration.

3. Configure Additional Stores
For all other Shopify POS locations:

Do not enable the "Store as Master Data" option.

Disable automatic cost syncing to QuickBooks.

Set sync mode to manual only for cost updates.

4. Perform or Schedule Syncs
Manually trigger the sync for the master store when cost or inventory updates occur.

Avoid enabling automatic recurring syncs unless all configurations have been carefully reviewed to prevent conflicts.