Q. I heard that for new tomatoes seedlings you should pinch off the first and second true leaf sets when they appear, without damaging the top growth, to strengthen the seedling. Is this true? What is the correct way to prune them, and what about other seedlings, such as cucumbers, mellons, peppers, etc.?
A. No! You do not want to take those leaves off at all – until more leaves have grown and are handling the photosynthesis. Then, after you have transplanted out of the crowded flat they were germinated in, and after leaves start overlapping the leaves of other plants, only then do you begin to prune any leaves.
At the first pruning, you will usually be taking two of the oldest leaves, and leaving 3 or 4.
Removing the existing leaves is a shock to the plant, and will stop it’s growth temporarily. This is actually desirable, if you have no space to continue transplanting into larger pots, and weather is not yet conducive for transplanting into the garden. As a general rule, you should remove less than 50% of the leaves at any one time.
And after two prunings you should transplant into a larger pot, and thereafter, separate the pots to give all plants full access to the direct sunlight.
Other varieties of seedlings generally do not need pruning as much as tomatoes, but it serves the same functions.