When it’s time to repot your tomato seedlings, go deep. In other words, plant it so a couple inches of stem is buried, as shown in the drawing.
How do you know when it’s time for repotting? Do it when your seedlings are about 4″ tall — or have their second set of “true” leaves. What is a “true” leaf? It looks like the leaves on the mature plant. The first set of leaves are usually simplified leaves, often called “seed leaves” or cotyledon.
When it’s time to transplant your seedlings into the garden (or outdoor planters), use the same technique. Sink the seedling an inch or two so it will develop roots along the buried portion of stem. Some gardeners even plant them at a 45-degree angle because, they say, it adds more stability as the roots develop.
Tomatoes are unique in their ability to generate roots along their stems. Most plants do not produce roots from stem tissue, so burying a plant’s stem will usually cause rot or even the death of the plant. As a general rule, a plant should be replanted at the same depth it was growing initially. This holds true whether you’re transplanting zinnia seedlings from a 6-pack, a shrub in a two gallon pot, or a tree that’s been ball-and-burlapped.
For complete details on transplanting tomatoes, read How to Repot a Tomato Seedling.