My business paypal account's primary currency is EUR. However, all my transactions are in USD. When I link the paypal with quickbooks, the transactions in USD are in EUR

I'll be glad to provide some insights about currencies in QuickBooks Online, @useraccounts14.

Once you connect your Paypal account to QuickBooks, the transaction will show the home currency. The default value for all customers, suppliers, and accounts is your company's home currency. You can manually assign the currency to the transactions. 

To learn more about multicurrency, feel free to check out this article: How Multicurrency works.

Feel at ease to let me know if you have other queries. I'll be happy to help you. Have a nice day.