In order to produce the best results, only prune plants that have reached at least 6″ tall. Any smaller, and you risk stunting the growth of the plant (or ultimately killing it, if it is small enough.)
For seedlings that are roughly 6 to 10 weeks old, top the plant by cutting all branches down to the main stem, leaving about 1 inch on each branch. You can leave one or two shorter branches intact, if you would prefer to. Many times, only the top/middle of the plant is cut back; lower branches are left.
These branches are later pruned or buried when planted, but they help to feed the plant during the pruning/regrowth period.
If you intend to ripen existing fruit before cold weather arrives, find the last set of fruit on a branch (aside from those much too small to stand a chance at growing/ripening), and cut just above the fruit you’d like to keep. Keep plants topped in order to prevent the growth of new flowers or fruit, which will require even more energy.
Protecting Freshly Pruned Tomato Plants and Seedlings
Pruning a plant is a stressful event. When you prune, be sure to avoid promoting additional stress. If it’s early spring, you’ll want to keep your plants protected from frost, as this could kill the seedlings very quickly.
Heat and excessive sunlight can also be detrimental, largely for seedlings that are not used to the heat or light. Do not prune your seedlings immediately before hardening them off; instead, prune them a week or two in advance.
If your outdoor seedlings seem stunted after pruning, you should make sure that their sunlight, temperature, watering, and nutrient needs are being met. If they are in small pots, the pots’ soil may be void of nutrients; if the plants consistently sit in a pool of water, they may over-watered. A lack of light could cause issues, as well.