Trim young pepper plants for the first time when they reach four to five weeks old and 4 to 6 inches in height. Count the first five full-size lateral leaf stems up from the bottom and lop off any of the main stem and leaves above that point.
Prune back established and pepper-bearing plants as needed to keep them from coming into contact with the overhead light source. Preserve a roughly 1-inch gap between the top of the pepper plant and the AeroGarden unit top.
Trim off any dead or discolored leaves or stems immediately when you see them. Inspect the pepper plants every few days. Look up from the underside of the plant, as dead leaves can hide here. Remove them as well.