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Saving Tomato Seed in Seven Easy Steps

Saving tomato seed is deceptively simple, Friends.

Yes, you can simply separate each seed from the fruit, rinsing and drying them before tucking them in an envelope to sow next season. 

But here’s the thing: That clear membrane surrounding each seed is full of anti-germination compounds. Unless that membrane is removed, only about 30% or so of your seeds will germinate. Which isn’t the worst, but it’s far from the best. 

For thousands of years our ancestors have fermented tomato seeds, effectively neutralizing those anti-germination compounds as well as removing some seed-borne diseases. It’s a gloriously simple process. 

1. Harvest ripe tomatoes. 

Once tomatoes are fully ripe, the seeds inside are fully mature.

Saving fruit from your best plants is essential. The healthiest plant, the most productive, most disease-resistant, most delicious: This is the plant you want to feed — and by fed by — for generations to come. You’re selecting seed as well as saving it.

Once a plant has clearly become infected with disease, resist saving its seed. (Here is the best way to prevent tomato disease.) Also, if the skin of your tomato has cracked, don’t let it stop you from saving its seed — unless you are making selections against cracking, which I hope you do

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Ripe tomatoes, whether they’re purple, green, yellow, red or rainbow, are full of ripe, mature seeds ready to save. (This is our Chiapas, by the way.)

Tomatoes are self-pollinating, with flowers that contain both male and female structures, and they largely pollinate themselves. That being said, if you’re committed to maintaining a variety without any potential of it crossing with another, make sure that variety is at least ten feet away from any other tomato variety. We keep at least fifty feet between tomato varieties, mostly because we like to sleep at night knowing the seeds in your packets are exactly as you expect them

2. Squeeze out seeds, enjoy the fruit!

Squeeze your seeds into a clear glass jar, allowing you to watch the process and know when the fermentation is complete. Pulp will inevitably fall into the jar and don’t sweat, everything will be fine.

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Have your cake and eat it, too; save your seeds and eat your salsa!

Enjoy the rest of your tomato as you dream of all season: in salsa, on a salad, as fresh pasta sauce, in ratatouille. Have your cake and eat it, too!

Indeed, so often in seed saving, we have to choose between enjoying a meal and saving our seed. We eat the pea or we save the seed — we cannot have both. Most of the time. Tomatoes are a glorious exception, as are ripe peppers, watermelon, cantaloupe and winter squash! We can have our cake and eat it, too. Save our seed and eat it, too

3. Label your jar

Tomato seeds in their fruit are quite distinctive. I can certainly tell a Gold Medal tomato from Gardener’s Sweetheart! Without their characteristic flesh, tomato seeds become quite homogenous and difficult to tell apart. I can’t tell you how many tens of thousands of seeds I’ve made anonymous across the years by not labeling well — so learn from my heartache, Friends. Label with name as well as date, so you can keep track of the process.

4. Add water to seeds & cover to ferment.

Now that you’ve got tomato seeds and pulp in the bottom of your jar, add an equal part water. For example, if you’ve 1/2 cup of seeds and pulp, add 1/2 cup water to the mix. This allows the fermentation to separate clear layers of mature and immature seeds.

Your resident fruit flies are delighted you’re saving seeds! To keep them at bay, cover your jar with a napkin and rubber band to exclude their enthusiasm.

Leave your jar on the kitchen counter — or any other easy place to remember their existence — for a few days.

5. Once layers separate, rinse well.

Now for the alchemy — my favorite part! — the fermentation itself.

The naturally occurring bacteria that exist on everything will proceed to metabolize the sugars in your tomatoes, causing pH and other shifts in the jar that we loosely (fondly!) call ‘fermentation.’ The clear membrane surrounding each tomato seed breaks down in this acid environment, mimicking the digestive tracts of animals eating tomatoes across time as well as the glorious decompositional ‘ferment’ that happens on the forest floor of Central America, the tomato’s place of origin.

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As fermentation progresses, mature seeds fall to the bottom and immature seeds rise to the top, along with the pulp. 

Tomato fermentation takes from 3 to 5 days, depending on the ambient temperature. Fermentation is faster in warmer conditions than cold, so expect less time in the height of summer and longer time as autumn descends. 

Once the fermentation is complete, three distinct layers will appear. On the bottom, you’ll find the dense, mature, fully ripe seed. On the top is the light, immature seed and pulp. In the middle is a layer of mostly clear water that may be red, yellow or orange, depending on the color of the fruit. 

Pour off the top layer of pulp and immature seeds, as well as the middle layer of water. Once you get to the dense, mature seed at the bottom, add a few inches of water to the jar once more. Continue to decant — adding water and pouring it off — until the water running off is completely clear.

6. Dry

It is important to dry any seed as quickly as possible. This allows your seed to maintain its quality for many seasons to come.

To dry your seeds, tuck them in a single layer on a screen, paper towel or any other surface that allows airflow on all sides. Leave them in a warm place out of direct sunlight with plenty of airflow. Between 70 F and 90 F is ideal for temperature, the warmer the better. Place a fan a few feet away to blow, wicking away moisture from your seeds.

If your tomato seeds are anything like mine, you’ll have some clumps. After a day or so, once these dry a bit on the outside, break them up so they’ll dry more evenly. I rub them between the palms of my hands. It is ever so satisfying

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Dry seeds on screens, paper towels or other surfaces allowing airflow; break up any clumps after one day, to help your seed dry evenly as well as quickly. 

To dry, one week is a solid minimum, though the actual time may be less or more depending on ambient temperature and humidity. If you have two pairs of tweezers, test a few seeds to be sure they break rather than bend when you put pressure on both sides. If your seeds are dry enough, they break. If they need more time to dry, they bend.

People often ask me if dehydrators are effective for drying seeds and the answer, sigh, is mostly no. Dehydrators ‘cook’ rather than dry seeds, unless you’re simply using it as a set of racks with a fan running on the bottom, the heat completely turned off. Any temp above 95 F is likely to frizzle your resilient yet delicate next generations.

7. Store and share!

Store your tomato seeds like any other seeds and here are the keys plus a sweet infographic for you to download! Desiccant packets are an ace up your sleeve, helping reduce humidity even more. You’ll find little desiccant packets in vitamins, shoes and seaweed snacks; we use much larger and more effective desiccant packets. We share them here

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Desiccant packets wick away excess moisture, helping your seeds store longer. We share the ones we use here — they’re massive and do the job well for years and years.

Some tomatoes (like most cherries) are chock-full of gorgeous seeds while others (like Italian Heirloom and other paste types) have very few seeds. Either way, a few tomatoes saved will likely surround you with hundreds of seeds. 

Be generous with them, Friends! 

Share them with family and friends, neighbors and strangers. Share them with anyone who may take care of them!

Saving and sharing seeds is largely how our species has become ‘civilized’ and so abundant on planet Earth in the last ten millenia, though we’ve lost these skills and wisdom since the industrial revolution.

If we learn to save and share seeds again then maybe — just maybe — our species may to learn to take care of plants, ourselves, each other and our planet, to amplify abundance for all generations of all species to come.

So yes, save seeds!

And yes, share them as abundantly as you possibly can!

Sow Seeds & Sing Songs,

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& the whole Fruition crew


Don’t cry over cracked tomatoes! You can still save the seed, unless you’re selecting tomatoes to not crack, of course

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This is our super early, disease-tolerant and remarkably sweet Seiger tomato, by the way.


6 thoughts on “Saving Tomato Seed in Seven Easy Steps

  1. Your enthusiasm about a little seed is phenomenal.

    1. Thank you for being part of our community! -Sylvia and the rest of the Fruition Crew

  2. thanks Petra for the tips

    1. Thank you for being part of our community! -Sylvia and the rest of the Fruition Crew

  3. Hi. I did not know that when they are dry they break and bend if they are not ready. Thank you for the information on how to saving tomato seeds. Kindest regards from a reader in Sweden

    1. Thanks for being a part of our community! <3

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