Do you prune pepper seedlings? There isn't a right or wrong way to garden, and whether or not to prune peppers is a perfect example of this. We have different climates, sized gardens, and goals. Topping pepper seedlings is often done to encourage pepper plants to have more of a bush habit with stronger stems. To prune your seedlings, cut the main stem to just above a leaf. #howtogrowyourownfood #growinginthegarden #gardeningtips #vegetablegarden #pruningpeppers #peppers