Tomato Seed Fermentation – Is it Required?

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Robert Pavlis

Is tomato seed fermentation required? There are quite a few methods described on the internet for collecting and cleaning tomato seed, but which one works best? How do we define ‘best’? What works well for a commercial seed company may not be the best option for a home gardener.

A very common option is the ‘tomato seed fermentation’ method. Some say that it is absolutely necessary in order to get a high germination rate but not everyone uses it and they still claim to get good germination.

It is also believed that fermentation reduces pathogens on the seed. In this post I will look at the science behind collecting and cleaning tomato seeds.

Tomato Seed Fermentation - Is it Required?
Tomato Seed Fermentation – Is it Required?

Cleaning Tomato Seed

tomato seed showing gel around each seed
tomato seed showing gel around each seed

Each tomato seed is enclosed in a gel-like sac, which is surrounded by tomato flesh. The latter part is fairly easy to remove from the seed, but even if you wash the seed in a sieve, the gel sac stays attached.

Many sources say that tomato gel or flesh will inhibit germination. If this is true, any method that does not remove it, will  not work.  It is claimed fermentation does remove the gel.

Tomato Seed Cleaning Methods

Here is a list of some of the methods used to clean seed. Let me know in the comments if you use a different method.

Fermentation of Tomato Seed

You scoop out the seeds from a ripe tomato, and let the mush sit for 48 hours. Some people leave it a week but that will reduce the germination rate. The resulting mush, which now includes a lot of mold, is washed and the seeds are dried.

This is probably the most popular method on the internet and it is also promoted by some government sites.

Rubbing Tomato Seed

This method does not really have a name, but ‘rubbing’ is quite descriptive.

You remove the seeds from the fruit and rub each one individually on paper towels. The gel rubs off easily and you are left with fairly clean seed. The seed is then washed, dried and and stored.

This method works quite well, and does remove all of the flesh, but it is a very tedious method. That’s not a problem for most gardeners who only need a few seeds of each variety, but if you want to collect 100 seeds – you will be busy for some time.

I have used this method personally and it produced high germination rates for me.

The ‘Do Nothing’ Method

When I first heard about this method I did not believe it would work, but many people do use it.

Microbe Science for Gardeners Book, by Robert Pavlis

You extract the seeds, wash them under running water and dry them. Don’t use a paper towel because the gel around each seed sticks tightly to the paper once it is dry. To reduce this sticking problem use wax paper or a ceramic dinner plate.

What about the extra gel and flesh? You just ignore it.

According to the science we think we know, the flesh will inhibit germination and this method simply can’t work. But for some people it does work, so maybe this is all a myth? Maybe the drying process followed by several months of storage is enough to overcome the inhibition?

Tomato Detergent Wash Method

There are also several reports of treating the seeds with various home products like Clorax, backing soda, washing soda, and trisodium phosphate (TSP).

All of these products should help digest the flesh and produce clean seed. It is interesting that many people collecting heirloom seeds are organic gardeners, but when it comes to seed collection they have no problem using chemicals!

There seems to be no evidence that chemical treatment is any better than fermentation, which does not require the use of extra chemicals.

Direct Burial of Tomato Seeds

Extract the seed along with all the flesh, or even use the whole tomato. Bury it right in the garden so the seed sprouts next spring.

I am sure this works to some extent since I have seedlings popping up in the garden every spring, but it’s not very practical, in my opinion.

Testing Methods for Collecting Tomato Seed

I decided to run an experiment and test three of the above methods; fermentation, rubbing and do nothing. This video will give you the details of how the experiment was done and show you the results.

YouTube video

If the above video does not play, try this link:

The following are my conclusions, based on my conditions and the three cultivars I tested (Garden Treasure, Garden Gem and Early Girl).

  1. There was no difference between cultivars.
  2. All three methods produced excellent germination – 100%.
  3. All three methods resulted in good growth of the seedlings.
  4. Leaving the gel and flesh on the seed did not cause any fungal growth.


tomato seedlings growing well for all collecting methods tested
tomato seedlings grow well for all collecting methods tested

The gel and flesh from tomatoes does not inhibit seed germination, or cause mold to grow, at least not after a couple of months in cold storage. The do nothing method worked just as well as the fermentation method.

Best Tomato Seed Cleaning Method for Home Gardener

I think the rub method is probably the quickest and easiest method for anyone who is collecting a few seeds for themselves. It allows you to extract the seed, and dry them immediately, without the need to wait several days for fermentation.

Best Tomato Seed Cleaning Method for Larger Quantity

If you require a larger number of seeds, the fermentation method is best. For a larger number of seeds it is the method that takes the least amount of work and it produces the cleanest seeds. This method may also have some benefit in decreasing pathogens.

For more information on doing fermentation properly have a look at this post; Best Way to Collect Tomato Seeds.


What about diseases? Does fermentation reduce diseases better than the rubbing method?

Fermentation “can destroy bacterial canker and other seed-borne diseases”. The rubbing method will not eliminate diseases that are on the surface of the seed.

If tomato canker is an issue, fermentation should last 96 hours (4 days) at a temperature about 18ºC (65ºF). This long fermentation can cause injury to the seed but is off set by a reduction of disease.

Late blight is a major problem with tomatoes and “as far as we know, the pathogen does not survive asexually from one season to the next on dried tomato seed.”

In most cases, treatment for diseases is not required after a fermentation process.

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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

24 thoughts on “Tomato Seed Fermentation – Is it Required?”

  1. The ultimate “do-nothing method: (not suggesting: just noting) My brother rubbed seeds and bits of flesh from an Indigo tomato onto a paper towel and mailed it to me in August of 2013. I have stored the paper towel in the mailing envelope and grown tomatoes from those seeds every year since.

  2. somehow tomato seeds got into my washing machine and after going through a full wash cycle ended up in my gray water garden and started to grow all on their own and produced fruit. It wasn’t even intentional. and often they will just start to grow out of compost piles.

  3. You’re working much too hard. We take a tomato and hold it in its normal position, blossom end down, stem attachment end up, and slice the tomato across its “equator.” Then just squeeze the juice & seeds into a clear cup. You get about 90-95% of them, then if you want any still stuck in the locules (seed cavities), you can use the end of the handle of a spoon or fork. If you are seeding a yellow, gold or orange tomato, if you hold it up to the lights you’ll see any you missed.

    I have switched to 9 & 16 ounce cups for most tomatoes, or 2 ounce cups for some paste types or cherry tomatoes. The 9’s & 16’s share the same lid, which happens to have a straw slot ( + ) which lets out any pressure, and still allows a mold mat to develop.

    I give them 3 days and then pour the mold off and add fresh water and swirl it around, then pour it into a taller cup & pour off more gunk and repeat a couple times until the water is clear and any flesh or skin bits are gone, then add water again to get the seeds moving and dump it into a small strainer. I put either a small amount of a gritty toothpaste or a squirt of an anti-bacterial soft soap in it and rub the seeds around. Then I rinse them, press them to remove more water, then smack them into the palm of my hand. I squeeze them to remove the water (there’s a lot!) and then spread them out onto a Viva paper towel. I roll them up and then flatten the roll and tuck the ends in & fold it and label with the name & date.

    Hope this helps.

    • getting the seeds out isn’t a problem, mostly its… “I just gotta have those seeds” lol I must have saved over 1500 seed judging by the 2 to 3 hundred I counted from tow different tomatoes. The fermenting for 2 to 4 days works perfect. spreading them out on an unfinished cutting board soaks up the water. storing them in old medicine containers is perfect. Thanks for the thoughts.

  4. I have tried to let my fish eat the tomato meat and then scoop up the clean seeds (guppy) easier than most other methods and get nice clean seeds (what people want)

  5. A video on YT showed someone slicing up what looked like a fresh tomato. If it was starting to rot, there might have been fermentation. Then that person put the slices on some potting soil, covering the slices with more soil to perhaps 1/2 inch deep. some time later, at least a week or so… some sprouts were emerging. did the slices have time to ferment? no idea.

    The idea I did have is… if I want to save seed from this year’s crop, all i need to do is slice the tomatoes, dry the slices and save til next year. Then plant the slices to get sprouts. I’m experimenting with that process now with a Roma from the grocery store.

    Another point.. the video narrator was somewhere in southern California. the seeds did not go through and “winter freeze”


    this method is working for this guy… but if he is in India, its a much warmer growing season. Did the slices ferment? hard to say. Either way… it worked.

    With real winter in my area, I won’t have “fresh” tomatoes to work with. However, I’m pretty sure if you sliced some mature tomatoes in the fall and dried them, planting the slices like that should result in a nice batch of seedlings. I’m gonna try that this year.

    Shucks.. I’ll just try it with a store-bought one just to try it out.

    Thanks for this one.

  7. I soak the seed in water for a couple of hours, rub in a sieve under running water, soak in a weak ammonia solution for 20 minutes ( 1 teaspoon Janola in a cup of water), rinse, then dry on wax paper.
    Seed in now clean without gel
    I store the dried seed in envelopes in a biscuit tin in a cool cupboard in the laundry until the next season. I rarely have less than 100% germination.

    • I think that you may have missed a washing step between the “let mold form” and ” let the seeds dry”. If there is no washing step, the dried seeds would be covered with flesh ,seed gel and mold.

  8. As I have 3-4 favourite open pollinated tomatoes, I save tomato seeds every year. In my opinion, fermentation removes germination inhibitors and the gelatinous sheath from seeds. Also, it may treat some seed-borne diseases. My experience says that seeds saved using fermentation method remain viable for over five-six years. If properly stored, of course.

    • Yes that is the opinion of many, but clearly in this example it does not inhibit germination.

      I have seen no data on seed viability vs washing technique.

      • I have been using the fermentation method for 20 years and I have never used another. So I can not compare. But, I never had problems with the germination of my tomato seeds. On the contrary, my seeds are full viable after 6-7 years. The record is 11.

  9. As a child in india, we just washed the seeds dried in sun and planted
    Ll the seeds – most – same way
    One year with pumpkin our roof nearly caved in


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