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Saving Heirloom Tomato Seeds Through Fermentation

Forget seed catalogs, I’m shopping for my tomato seeds at the farmer’s market. Walking through the colorful displays of produce at my local farmer’s market, I’m brimming with anticipation for the next gardening year. The heirloom tomatoes that I pick out today—given they pass the all-important taste test—will be the garden bounty of my to save heirloom tomato seeds through fermentation

Saving heirloom tomato seeds brings back those memories of science classes: beakers and safety goggles, anticipation and disgust, curiosity and pride. The seeds can’t just be scooped out and dried; they need to be removed with all the slimy tomato guts and left to ferment. The gross factor of fermenting these tiny seeds is about as fun of a science experiment as you can get, making it an ideal project to do with kids.

Related: Getting Back to Basics with Seed Saving

Now you may be asking yourself, “Why on earth do I need to ferment the tomato seeds? Can’t I just scrape them onto a paper towel and dry them?!” The answer is that fermenting the seeds is copying the natural process the tomatoes would go through to reproduce. The membrane around the seeds prevents germination and can carry disease. By fermenting it, it sterilizes the seeds and thus protects the next year’s plants. In addition, it  gets them ready for winter storage so they will be primed for good germination rates when the time comes.

Here is What You’ll Need:



1. Choose Your Seeds

The most important part of saving heirloom seeds is selecting the best fruit to begin with. Whether you are purchasing your tomatoes or have grown your own, you should look for the best visual example of a variety: perfect color, size, and shape. Ensure there is no disease or pest damage visible, and don’t forget to taste them. Yummy tomatoes make seeds that make yummy tomatoes.

heirloom tomato varieties

2. Scoop Out the Guts

Gently cut your perfect tomato into sections.

tomatoes cut into sections for seed saving

Grab a spoon and scoop out the seeds and the gel-like membrane that they are surrounded by. This whole glob goes right into the Mason jar so it’s going to get a bit messy. Fill up each jar with about ¼ cup to ½ cup water, just enough to cover the goop.

fermenting tomato seeds in a jar

3. Cover and Label

Write the variety name on a piece of paper towel folded square, and secure to the lid by screwing on the ring over top. This allows for air to circulate to the mixture as it ferments, but also makes sure you don’t forget the variety.

covered and labelled tomato seeds

4. Store in a Warm Place

Now set the Mason jars someplace warm, out of direct sunlight where they won’t be disturbed for a few days. Depending on the temperature, it could take 2 days to a week so be prepared to stick around and keep an eye on them.

fermenting and saving tomato seeds

 5. Check for Mold (You Want Mold)

Within a few days, the top of the liquid should have a grayish rim of scum and even later, a full cover of mold. At this point the seeds should have sunk to the bottom of the muck as well. Congratulations! This means that the fermentation process is complete. This is also great news because the jars are likely smelling quite awful by now.

tomato seeds with mold cover

 6. Strain and Rinse

Add another ½ cup or so of water to the jars to dilute the gunk and allow the viable seeds to sink to the bottom. Gently pour off the top layer of fermenty-goodness and then strain the seed into a fine-mesh sieve.

straining tomato seeds

 7. Drying

Next, you need to dry the tomato seeds. Place the strained tomato seeds on a plate or bowl and set back in the warm dry place for a few days to dry out. Many people use paper plates, but my little glass bowls work just fine for me. Make sure that you attach or set your paper towel cover / label to the seeds – there is nothing worse than going through the process of fermenting seeds and then forgetting which variety they are!

drying fermented tomato seeds to save

 8. Storing

Once your tomato seeds are dry, you can shuffle them into some handy little coin envelopes, label them up, and store in a cool dry place until next spring. You have graduated from science-class geek to a true heirloom-tomato alumnus.

What’s an Heirloom, Anyway?

Heirloom seeds have been saved and passed on for many generations and so the plant, flowers, and fruit are true to type of the original great-great-great-(insert 50 years here)-grandmother plant. The seeds have been saved for their outstanding qualities, be it beauty, flavor, and yield, or disease, pest, and weather resistance. Heirloom vegetables and fruits provide much diversity from the standard fare mass-produced by industrial food production.

assorted heirloom tomatoes

There are many colorful and unique tomato varieties, but beauty and diversity doesn’t mean it’s an heirloom. Hybrid tomatoes have been created by cross-pollinating strong characteristics of different varieties, making brand-spanking new varieties. While the tomatoes can look and taste as good as heirlooms, saving these seeds comes with problems.

Some seed companies create franken-fruits that only contain sterile seeds, ensuring that you always have to buy from them. Even if you could save and germinate the hybrids, there is no guarantee what characteristics the new plant will have. Remember, they cross-pollinated before so who knows what they will get up to with the other tomatoes, nor what the offspring will be.

Hey! Now that you have your tomato seeds ready, how about some printable seed envelopes? Download them here:

Free Printable Vegetable Seed Envelopes from Garden Therapy


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  3. Just for the record, almost all tomatoes available at the supermarket, are identically reproduceable from their seeds, in particular, all the “grape” varieties, even thou some are hybrids – they still come true. Great blog!

  4. I save seeds only from “open pollinated” (OP) or heirloom tomatoes, because these are tomato varieties are true to their type from their own seed, which means the next season’s new plants will maintain the same characteristics as the previous one.

    • Actually this is not exactly correct, as if you do not know where the fruit and it’s seed were grown and under what conditions, then you cannot be 100% certain of the results… it could quite easily be cross pollinated and therefore the seed would NOT produce exact true to type plants and fruit…
      When commercially growing and certifying seed for type / variety, it has to be done under strict conditions so as to not allow for cross pollination of flowering plants. This can be achieved in various ways as distance planting of varieties, bagging or screening of crops etc. but are needed to be introduced to prevent cross pollination of TRUE TO TYPE varieties and Named seed types.
      So just using ‘bought’ fruit of a heirloom variety and using the seed DOES NOT produce for certain the variety of it’s heirloom parent… FACT.
      Even though it may or at least may look similar to it’s parent fruit. It also may just be a crossed plant bearing little resemblance or characteristics to the original. – so be aware.
      Jim (Orgasmictomato), grower, breeder, tomatoes. Au

      • Tomatoes cross only 4% of the time! They are self fertile. On rare ocassion you might get a cross like Dr. Carolyn Male RIP and Craig deHiliyer with OTV=Off the Vine Brandywine, a cross of Brandywine and ? Never mind if you are lucky enough to find the seeds, you too will fall in love w/another tomato. -Mary-Anne (TomatoMania)

  5. Great artical , I plan on trying this. I do have a question. After putting a folded paper towel on top of the jar you put the lid & ring over it & said that allows it to breath, do you just very lightly screw the top on? I wasn’t understanding how it would breath. Thanks for helping me understand this.


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