MyWorks supports tracking cost of goods sold in QuickBooks in several different ways, depending on how your products are managed in your QuickBooks Online company. 

When Inventory Items are present in QuickBooks

This is the most common scenario we see with our users. As long as your products are present in QuickBooks as inventory items; and mapped to your Shopify products in MyWorks Sync > Map > Products; QuickBooks will correctly record the Cost of Goods Sold for each order, when we create the invoice or sales receipt for that order in QuickBooks that includes that product. There's no additional action MyWorks takes aside from creating the invoice or sales receipt in QuickBooks.

A couple helpful tips to be aware of in this scenario:

• QuickBooks handles inventory costing on a FIFO basis, meaning that the inventory cost is recorded on a “first in - first out” basis: so the “oldest” inventory levels (and the associated cost they had when originally recorded in QuickBooks) are used up first.
• The cost that a QuickBooks inventory level is initially recorded with is super important. If the product was created in QuickBooks with an inventory level of 5 but a $0 cost, QuickBooks will treat those 5 quantities as having a $0 cost when they're ordered in the future. 

When Inventory Items are not present in QuickBooks 

There may be some scenarios where it's not desired or possible to have individual inventory items present in QuickBooks to match your Shopify inventory items. When this is the case, the COGS would not be recorded in QuickBooks when an order is synced, as there would be no QuickBooks inventory items used in that order.

However, MyWorks does support syncing a daily journal entry into QuickBooks to help record COGS, in this case. 

This can be enabled in MyWorks Sync > Settings > Order - and you can set the correct COGS and Inventory Asset accounts for us to use.   

Once selected, MyWorks will sync a single journal entry into QuickBooks each day to record the total COGS for the products ordered that day - as well as the reversal of COGS for any refunds that occurred that day.