Puppy sleeps fine in crate inside pen but cannot handle being alone at all

Hi everyone! My 3-month old chihuahua sleeps just fine in his crate, which we keep inside a pen in our bedroom, with the crate door open. The crate is super cozy and he goes in there by himself when we sleep. The problem is I am really struggling to teach him how to be alone. Even if I go to the loo for 5 mins while he is sleeping (or awake) in the pen, he cries a lot. We've been going to do our thing regardless of his crying but it doesn't seem to get better at all. Tonight we tried to leave him alone with a frozen kong, but as soon as he realised that he is alone started to ugly cry and pretty much ignore the kong. If we leave him in the living room alone for a few minutes during the day he still cries sometimes, but seems to be better overall with less crying and sometimes none at all. But our living room is too big and there are too many things he can destroy so we cannot leave him there for more than 5 mina without worrying that he'll do something stupid. I don't know how to proceed with time alone, his breed is prone to separation anxiety and I really want him to be able to be alone from time to time for a few hours eventually, but atm he can't even do minutes.

Any advice is appreciated! 🙂