If more than one tomato seed germinates in a single soil cell, you have 2 choices.
You can try to ‘prick out’ the seedlings, transplanting them into separate soil cells when they are still small or you can thin out the smallest seedlings leaving the healthiest one. It is very hard for any gardener to ‘kill’ one of their pampered baby tomato plants*, but for most, it’s the best course of action. Trying to separate tiny seedlings often leads to all of them getting damaged or their growth to be stunted. So, go ahead …. take out the scissors and snip off those extra seedlings at the soil. Don’t try to pull them out, you might damage the roots of the seedling that you leave behind. Your remaining plants will thank you for not disturbing them twice, since in most cases, tomato plants need to be transplanted into larger pots weeks before they can be planted into the garden.
Seedlings grown in 2” cells or flats will become pot bound and stunted, or take longer to recover when they are planted outside if they are not transplanted into larger pots at least once. 4” Cow Pots are the perfect size and are usually large enough to hold young plants until it’s time to move them out into the garden. With Cow Pots there’s no transplant shock since you plant them pot and all into the garden!
Pop out the seedlings to be transplanted from the bottom of the cells and handle them by the root ball or the leaves. Do not pull the seedlings from the cell which can rip off tiny roots nor handle them by the stem, which can easily crush and kill the plant.
See those little hairs on the stem? They will turn into new roots and give you much stronger plants. Remove any leaves that will be below the rim of the pot. Place the seedling in the bottom of the empty 4” Cow Pot (I like to wet the Cow Pots first).
Fill the pot with soil (you can use any remaining seed starting soil), water and add more soil as needed. Return the newly transplanted plants to the grow lights (which may need to be adjusted in height) and continue the routine of 14-16 hours of light.
Newly transplanted seedlings may not need as much water for a few days until the roots start to fill into the new soil. Fertilize weekly, and don’t forget to continue to pet your plants!
*Planting only one seed per soil cell avoids thinning all together. If the first seed planted doesn’t germinate within a week, plant a new seed in the same cell. A few days delay compared to the other seedlings won’t make much difference.