Decide whether you need to conduct early or late-season pruning. Look at your plant and determine whether you need the existing peppers to mature before the end of the cycle, or whether you want larger peppers next season.
Wait until the plant is a foot tall, if you plan to prune early in the season.
Notice the plant's shape. It will have an overall "Y" shape, with smaller "Y" shaped formations branching out from the main part of the plant. Using your pruning shears, trim off any small branches, as well as any branches that grow in the middle of a "Y."
Wait until the first frost of the year is just a few weeks away and evaluate the plant to see which bell peppers have a chance to ripen before the end of the season.
Remove any flowers and peppers that do not fit this criteria. This allows all the plant to focus all of its nutrients on the most viable produce.