saving tomato seed: a day at hudson valley seed

'Upstate Oxheart' heriloom tomato at Hudson Valley Seed Library farm.SEED LIBRARY CO-FOUNDER DOUG MULLER makes it sound easy, and gross in a fun way—you know, like when you’re 12 years old and “gross” is a good thing, an adjective you say and then giggle delightedly at the slightly naughty notion.  The co-founder of Hudson Valley Seed was teaching a group of us how to save tomato seeds, using words like “slimy” and “smelly” and “goopy” and, yes: “gross.” How to save “wet” seeds such as tomatoes, the Hudson Valley Seed way. (That’s one fruit of their ‘Upstate Oxheart’ heirloom variety, above.)

Harvested tomatoes at Hudson Valley Seed Library, August 2013.I spent another day at Hudson Valley Seed in Accord, New York one late August, where I gave a lecture as part of their annual farm tour. You can visit them anytime online, and learn about growing vegetables, herbs and flowers and saving their seed on the seed company blog. Because they’re a small farm, they don’t use lots of seed-processing machinery, but rather the kinds of tools a home gardener would use (though maybe the slightly larger size, like the size-XL masher, below).

Giant masher for processing wet seed, at Hudson Valley Seed Library.With wet seeds—ones that come enclosed in a fruit (the part of the plant we eat, such as tomatoes, tomatillos, eggplants, peppers, squash and cucumbers)—the process is roughly the same, though some are “wetter” than others with more obvious seeds.

Yes, you could simply separate seeds from the pulp and skip the smelly-gooey-gross part of the process. But that part–the natural act of fermentation that’s happening in the jars in the photo below–helps break down germination-inhibiting compounds such as the gel sac around tomato seeds, and can also reduce some seed-specific diseases.

Tomato seed fermenting at Seed Library.let’s save some tomato seeds:

Select a few of your best-looking mature fruits from each of your healthiest-looking plants. The variety must be open-pollinated, sometimes called “heirloom,” and not a hybrid. It should also have been isolated from another tomato variety by at least 25 to 50 feet. to avoid cross-pollination. Choose fully mature fruits that look like the variety is supposed to.

If the tomato fruit is a little past peak ripeness, no worry: Nature saves and re-sows her own seed when the over-ripe fruit falls onto the ground and rots in place, Doug reminded us. “We just simulate that,” he says. (Side note: With squash and cucumbers and eggplants, you need to let the fruits get overripe first, probably a few weeks past good eating stage.)

Tub of fermenting tomato seeds, at Hudson Valley Seed Library.Quarter the tomatoes, squeezing the innards (seeds and pulp) into a container. A large canning jar may be plenty for the home gardener; at Seed Library there are giant plastic tubs in use everywhere (like the one above), full of festering “wet” seed pulp. (Remember he warned us it would be gross!)

Reserve all the tomato flesh in a pot or your food processor bowl, to make sauce or soup or salsa or gazpacho.  (With eggplants, squash and cukes, the leftover flesh at seed-saving time won’t be usable as food.)

Add water to your seeds and pulp to create a concoction that’s equal part fruit and water, and set it aside (but not out in the sun; a shed is perfect), covered with screening or cheesecloth to keep bugs away.  Allow the mashup to sit and ferment for about three to five days.

Keep a close eye so that it doesn’t go too far and over-ferment!  Depending on temperature, timing can vary batch to batch. The clue: Once a smelly scum or mold forms on the top of the mix, it’s time to wash the seed clean, said Doug.

Skim off the mold, in which will probably be floating some seeds. Discard those, too; floating seeds are non-viable, and the good ones will have sunk to the bottom.

Put your mix in a strainer and wash thoroughly. Empty clean seeds into an unwaxed paper plate (labeled as to variety) and allow to dry thoroughly. If it’s humid out, run a fan on low nearby.

Store thoroughly dry seed in a cool, dark spot in an airtight jar—and again, label them!

Doug Muller in spirtime at Hudson Valley Seed Library


connect with the seed library

'Upstate Oxheart' tomato packet from Seed LibraryHUDSON VALLEY SEED, a shared passion of Doug Muller (above) and Ken Greene, sells organically produced open-pollinated seed in the most beautiful seed packets anywhere.


  1. Nadia@Loveliveandgarden says:

    Great information! What a beautiful tomato that is also!!! My 6 year old son thought it was a pumpkin!

  2. Amy says:

    Can you explain what you mean by “unwaxed paper plant” for drying seeds? I just realized you might have meant plate. Is that the case? Thanks for the tutorial!

  3. Susanna says:

    This was very interesting and something I am going to try. I was, however, a little confused.
    “Put your mix in a strainer and wash thoroughly. Empty clean seeds into an unwaxed paper plant (labeled as to variety) and allow to dry thoroughly. If it’s humid out, run a fan on low nearby.”
    What is an unwaxed paper plant?

  4. CityGirlCountryBloke says:

    Thank you, thank you, thank you! You must be a fly on the wall in my house because we were just discussing how to make seeds for planting from our tomatoes. This is very informative and helpful for novices like us!! Thank you!!!

    1. margaret says:

      Glad to help, CityGirlCountryBloke. The Hudson Valley Seed Library (though not near you!) always teaches me good lessons that I love to share.

  5. Abby says:

    I’ve always saved tomato seed the easy way -1. choose the ripest most fabulous healthy tomato in your garden. 2.cut it open 3. spoon out some seeds with their juice 4.place on a piece of clean paper towel 5. label it 6. put it in a dry spot, loosely covered 7. eat the rest of the tomato.
    in a few days the paper towel will be dry. put it in safe protected place (like a zip lock bag in the freezer) In the spring you can scrape off the seeds and plant them. I have had 95% germination with this method, even using seeds that were several years old. and no more than the usual disease problems

  6. Janna Makaeva says:

    I am with Abby, have been saving my tomato seeds for years using much simpler method! Scoop on the paper towel as is, or into a small strainer and rinse the flesh off. Let dry on a paper towel. Eat the rest of the tomato. Sometimes I use over-ripe, slightly fermenting tomatoes in the first place for seed-saving.
    No germination issues ever (usually about 100%) and no diseases with this method.
    Why go through this gross stinky mess? I see when nursery is doing it for huge quantities of seeds, but for a home gardener?

    1. margaret says:

      Hi, Janna. The advantage is that some seed-borne pathogens are killed in the fermentation, plus any germination-inhibiting material is fermented away as well, so your germ rate may be higher. No worry otherwise, but it’s nature’s way — to let the fruit rot first, before the seeds escape and are dispersed, so the fermenting is part of the natural process the plant “recommends” if we wish to mimic its process.

  7. Kate says:

    Thanks for this thorough instructional! Another source I trust uses glass jars (smaller scale) and same method, but he seals his jars indoors to avoid the smell and bugs while they ferment, giving ’em a shake once or twice a day. I appreciate learning this “open air” method you’ve posted! And am ogling that pretty seed rack in the picture. :)

  8. Patricia says:

    I do container gardening so my plants are not the required #feet apart but will save seeds from my best efforts anyway. I’m using last years seeds and have fantastic results with the largest grape tomatoes yet. Good info here and thank you. :)

  9. Caren HAZELWOOD says:

    I harvested seed with success by letting one tomato ripen on the vine and then rotting there too.

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