Is there a possibility in Spryker that I manually log in customer. (For example once the email is confirmed) tried with

src/Spryker/Client/Customer/CustomerClient.php::setCustomer

while isLoggedIn returns true after that, I still cant access the protected pages. Probably need something else

The login is done via Symfony, so you can create an authtoken and persist it in the token storage. https://github.com/spryker-shop/customer-page/blob/master/src/SprykerShop/Yves/CustomerPage/Authenticator/CustomerAuthenticator.php#L45 provides all you need to login a customer.

Thanks!