[bitpow]

My son started making games in Scratch at around 8 or 9. He eventually graduated to Pico-8 and at 12 that is still his preferred tool for making games.

A few threads here recommend pico-8, however, you said he specifically wants the game to be 3D.

The developer of pico-8 has another project named Voxatron which is similarly accessible like pico-8, but for 3D gaming.

Worth a look: https://www.lexaloffle.com/voxatron.php

[bit_shifter]

Voxatron is what came to mind for me given OP's requirements. I own it but still haven't used it myself, but given it's from the same group as pico-8, I would bet it fits the bill perfectly.