Hello everyone,
I aquired myself some seeds for a Dwarf Pomegranate tree (Punica Granatum) some time ago, and planted them following instructions I found online. After the seeds had begun sprouting I moved it to a bigger pot. I am however unsure if I should prune some of the lower leaves of my seedling, or if it may be too early. It has been growing for around 3 months now.

Hello and welcome.
You should let it grow for at least two years before attempting to do any pruning.
It needs strong roots and a trunk (not a fragile stem).

You can however put a little shape in the stem using a thin wire. Doing this later will be more dificult. Just be carfull.. THe stemm is very brittle.

I too have obtain a young pomegrenate from seed about 3 months ago, although it is much smaller. Is there a way to ''force'' the tree to produce a larger trunk? Should I remove the terminal leaves?

Only way to grow a trunk is to let the plant grow. For this, there are many different routs. But in principle it comes down to: More leaves, more stemthickness. Longer stems = more thickness

Hello

Good to see other are also growing pomes! i have grown a few in my time, currently have them aging from 3 yrs old to 12 yrs old all grown from seed.

Its best to leave the baby plant for the first 2 years with light wiring to obtain best shape you desire. This us much easier while tree is young and goes get pretty hard as the trunk hardens. Help the plant grown as big as it can and only trim any shoots that are getting too long.

Ill post some pics from my phone to give you an idea how mine look.

Here you go