That's definitely a tough spot to be in! We went through a very similar situation last year when we connected Shopify to QuickBooks and suddenly saw income statements go haywire. QuickBooks pulled in all this old data I didn’t need, auto-categorized it in ways that didn’t match my setup, and created a mess of new accounts and duplicate sales.

What worked for me was disconnecting the native Shopify integration (you can do this from the Apps tab in QuickBooks), and then builk-deleting the duplicate transactions it had added—definitely a tedious cleanup, although I also considered just starting a new/fresh QuickBooks company.

After that, I switched to using MyWorks Sync to connect Shopify and QuickBooks. It’s been a total game changer. Unlike the native integration, it lets you:

• Set a specific start date, so you can control exactly what data gets synced.

• Customize how your orders and payouts are categorized.

• Choose between syncing individual orders or summarized daily/monthly entries—so it's way easier to keep pop-up sales separate from online ones in your reporting.

I now have it set up to sync just a daily summary for each sales channel, which keeps my income statements super clean and accurate.

If you're looking to keep better control over how your Shopify data shows up in QuickBooks, I’d definitely recommend giving MyWorks a try. Happy to share how I have it set up if that helps!