Trial and error. Seeing what other animals ate. In the mountains of Tibet, herdsmen noticed that when their herds grazed on caterpillar fungus, they were noticeably more lively, energetic, and could stay on the move for far longer. This made them try it out for them selves.

Other tribes have more whacky explanations, like the makers of ayahuasca, said it was the jungle that told them how to make it.