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You should wait to prune the plants until they are getting 6 or more hours of sun a day and they are filled with blooms. Once blooms start to die, you can start deadheading. Unlike deadheading by hand, the plant will do best with a sharp cut. Choose 1 that has several dying blooms on it. Find a point just below all the dead blooms. Aim to prune them below the majority of the spent blooms, if possible. Although you must cut back portions of a healthy plant to encourage new, thick growth, pruning petunias will extend your growing season. Doing regular pruning will help you avoid pruning off all your stems at once, making them look bare for a few weeks. Occasionally, you will need to prune off a healthy blooming stem. If a stem is looking long and leggy with lots of dead blooms, sacrifice the healthy bloom on the end so the plant will bloom longer. If possible, do it right before you leave for a trip, so that you will return when the petunia returns to full bloom. Do it after a pruning session to encourage new growth.
Allow your petunias to start blooming. Get a sharp pair of pruning shears or scissors. Pick up a petunia stem gently. Cut up to 1/2 of the petunia stem with your sharp shears. Prune 1 stem weekly on a small petunia plant, or prune 8 to 12 stems in a large hanging basket. Time a large pruning session for mid-summer, if you were not able to do it weekly. Fertilize petunias with a liquid fertilizer every 2 weeks.