Why and How to Transplant Tomatoes (a Second Time)

You might be ready to graduate your tomato plants to the garden, but transplanting tomato seedlings a second time only makes them stronger. That's because burying tomato stems (again) encourages them to grow even more roots... and more roots mean bigger, healthier plants that are better able to withstand pests and diseases.

Written by Linda Ly

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I’m at it again… transplanting tomatoes. The seeds were started indoors in newspaper pots. The healthiest seedlings were repotted into 4-inch pots once their true leaves appeared.

Now, those seedlings (teenagers in tomato years) are being transplanted into 1-gallon containers.

We’re more than a month into growing tomatoes, and while they can technically graduate to the garden by now, I prefer to transplant them into larger pots one more time.

What’s the point? you might be asking. Why wouldn’t I just start my tomatoes in large pots, and let the roots grow unbound until they’re ready to go in the ground?

Because every time you transplant your tomato, you sink the lower portion of its stem deeper into the soil.

It’s really worth the extra effort, and I’ll tell you why.

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Tomato stem primordia (tiny bumps on the stem that are the earliest stage of root development)

How and why burying tomato stems gives you more roots

Tomatoes have a special trick up their sleeve: the ability to grow new roots (adventitious roots) along any part of their stem.

Given enough moisture and light, these roots emerge from tiny bumps (also called root initials or tomato stem primordia, the earliest stage of root development) and can actually grow without soil.

If you live in an area with high humidity or you’re prone to overwatering your tomato plants, you may have seen the bumps turn white and become more prominent.

This tendency of tomato stem primordia to appear so easily can be used to your advantage.

By partially burying the tomato stem when you transplant a second time, you’re anchoring the plant more firmly in the soil and encouraging even more roots to form. Having a deeper, greater mass of roots helps your tomato plant be more resilient against wind, drought, pests, and diseases.

Tomato seedlings ready to be transplanted

How many times should you transplant tomatoes?

If you started your tomatoes early from seed and have some time before they go in the ground, it’s a good idea to repot them two or three times as they develop. Doing so builds up a bigger and stronger root system, as their vigorous taproots can grow up to 1 inch per day.

While tomatoes may suffer a small amount of transplant shock, they recover quickly and transplanting ultimately stimulates their growth.

Tomato transplants in 4-inch pots in the sun

How big should a tomato plant be to transplant?

Generally, the right time to transplant is when your tomato plant reaches three times the height of its container. So if you’re moving from a 4-inch pot to the next size up, wait until your plant is 12 inches tall so there’s enough stem length to bury.

The progression of pots should go like this:

Seed starting pots (or soil blocks)
4-inch pots
1-gallon pots
Final container or garden planting

If you’re growing tomatoes in pots, the final container size should be 10 gallons (for determinate types) or 20 gallons (for indeterminate types).

If you’re growing tomatoes in the ground, plant them at least 18 to 24 inches apart (more space is always better for proper air circulation).

Can you transplant tomato plants with fruit?

Technically speaking, yes, you can transplant tomato plants with fruit or flowers. As long as the plants aren’t severely root bound in their pots, they’re quite hardy and should recover easily from any transplant shock (whether in a pot or in the ground).

If your young plants are already loaded with blossoms, however, they stand a better chance of surviving a transplant if you remove all the flowers and fruit first.

This may sound counterintuitive, but a young plant that’s already flowering and fruiting is responding to stress. It’s putting all of its energy into producing seed so it can spawn the next generation of tomato plants. This means it focuses more on producing tomatoes and less on growing new branches and leaves.

Letting a young plant flower and fruit in this early stage could stunt its growth or delay production of more fruits. By pinching off the flowers before you transplant, you help it focus on vegetative growth so it can photosynthesize and grow strong and tall before it starts to flower abundantly.

Transplant tomatoes for more vigorous growth

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How to transplant tomatoes in pots (a second time)

Step 1: Start with clean pots and fresh potting soil.

For the second round of transplanting, step up to 1-gallon pots. They don’t have to be disinfected first (in fact, I advocate for not washing plant pots), but they should be clean and free of disease.

(I used black plastic pots in these images because I had a lot of them around the yard, but if you can get your hands on 1- or 2-gallon fabric pots, my current recommendation is to use those instead. Fabric pots air prune the roots and make them even stronger.)

Related: Best Grow Bags for Your Garden

Have plenty of well-draining, well-amended potting soil on hand. I recommend mixing your potting soil with compost, or stirring in a granular tomato fertilizer before you plant (following the package instructions).

If you have a lot of transplants to pot up, it’s often more cost-effective to make your own potting soil at home.

Tomato plants in 4-inch pots, along with 1-gallon pots

Step 2: Pinch off the lowest sets of leaves.

With your fingers or a pair of garden scissors, pinch off the lowest two or three branches of leaves, especially if they’re wilting or yellowing. You will end up with a tall skinny stem with only a few branches on top.

Pinch off the lowest branches on the tomato plant

Step 3: Loosen the root ball and place the tomato plant in an empty pot.

Carefully loosen the root ball and place the transplant in an empty pot. The rim should be just below or even with the branches.

While it’s true that the roots are sensitive, they are not the most vital part of a tomato plant—the stem is. New branches, leaves, and roots continue to grow throughout its lifespan, but a tomato plant usually only has one main stem.

The plant cannot sustain damage to the stem, which should be treated with care during transplant. Handle the plant gently by its leaves or root ball, but avoid manhandling the stem.

Gently loosen the root ball of the tomato plant

Tomato plant placed in the bottom of an empty pot

Step 4: Fill the pot with potting soil.

Fill the pot with potting soil, all the way up to its lowest branches. Give the pot a good final shake and add more soil as needed to stabilize the stem.

Resist tamping down on the soil with your hands or trowel (watering will do the work of settling everything in).

Fill the pot with high-quality potting soil

Give the pot a good shake and fill with more potting soil as needed

Step 5: Water the tomato plant deeply.

Your newly transplanted tomato should have several inches of stem sunk below the surface. Water deeply down to the lowest roots and only water again when the first 2 inches of soil feels dry.

With a deep-rooted plant like tomatoes, the key is to water less frequently, but more thoroughly. Tomato plants like to be slightly dry in between watering and they will not tolerate being overwatered, so try to keep the moisture level consistent.

Over the next few weeks, feed your tomato plants with an organic slow-release fertilizer as needed.

When your plants have grown two to three times the size of their pots, you can transplant them in the garden, again pinching off the lowest branches and sinking the stems deeper into the soil.

They’ll be pretty tall so a transplanting trick to save your back (from digging all day!) is to transplant your tomatoes sideways in a trench.

By repotting my plants a second time, I’ve found that my tomatoes have a head start on the season and flower much sooner… bringing me that much closer to a summer full of juicy, ripe tomatoes (along with fermented salsa, fresh tomato sauce, and oven-dried tomatoes!).