Fill a 3- to 4-inch pot with potting soil, after the tomato seedlings have produced their second set of leaves. Prepare a separate pot for each seedling you are repotting.
Lift the seedling from the seed flat by the topmost leaves. Plant the seedling in the new pot so it sits 1 inch deeper than it was growing at in its previous location.
Water the newly repotted seedling with warm tap water until the soil is evenly moistened but not soggy and wet.
Repot the seedlings a second time into 6-inch diameter pots once the seedlings are about 8 inches tall. Plant the seedlings 2 inches deeper than they were at previously. Tomatoes produce roots along the buried stems, so planting deeper encourages the plant to produce a larger and more healthy root system.