I also dig under and let the Elder try to play whack-a-mole with me, except this mole has fire arrows.

You can dig a hole under all four sides of the altar or just two sides, and have them meet up in the middle. I usually run back and forth between two entrances. Make sure there's enough room in your side ditches to get around any roots that sprout up, but better yet, run under when you see him raise his hand. Prime the bow before you go outside. Alternate between fire and flint because there's no point in stacking fire on top of itself.

If you're lucky, he might spawn in one of your ditches and then it's even easier.