I have Stripe set up to connect with Quickbooks on through our online store. I think the stripe sale and stripe deposits are both being counted though.

Hi kmccarthy,

Thanks for reaching out to us here. QuickBooks is a versatile program that offers the flexibility you need to process Stripe payments. I'll be happy to steer you in the right direction so you can the support you need. 

To get started, are you by any chance manually recording the deposits in QuickBooks? The reason I ask is that some apps will automatically enter the deposits for you. This may be a reason why the deposits are doubled. Did this just start happening or it's been like this? You can delete a deposit in QuickBooks by opening it > clicking on More at the bottom of the screen > Delete. 

Give this a try and let me know what happens. I'll be on standby in case you need anything else. 

@kmccarthy 

Consider having a connector to reconcile Stripe transactions to your QBO account and avoid any duplication.