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.

Compost Science for Gardeners 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. Hi, great post :). The (small scale) plant nursery I worked for did the following: they took a piece of newspaper and spread out the gelly seeds flat on it with a spoon. Then, once air dried, the seeds fall off more easily than from a paper towel. This worked well for some Cultivars and some did have trouble germinating. Stored dry and cool (I usually just fold the piece of newspaper and label it for storage) there never was an issue of mold or insects. If you‘re not selling or trading seeds it might perhaps also work for some people to see how your cultivars are doing first – and then ferment seeds if they have trouble growing. I can‘t say exactly with ours, because it‘s possible that they did not collect seeds from enough individual plants for enough genetic varitation in their seed (which can also cause trouble in reproducing good quality seed over time).

    Do you perhaps know something about how many Tomatoes of the same kind I need to grow to ensure Cultivar stability over time ? Still trying to find something about this.

    Thanks 🙂

    • “Do you perhaps know something about how many Tomatoes of the same kind I need to grow to ensure Cultivar stability” – sorry, no. It is going to depend on how stable the genetics is when you start. And one can argue that you never get genetic stability – so how you define this also affects the number you need.

  2. I wash them in a strainer then scrape them onto a paper towel trying to space them out and make a straight line. Before spring the next year, I tear off a piece of paper towel with a couple seeds and plant that. I have never had a problem in my 50 years of gardening.

  3. If all 3 methods had 100% germination, and the do-nothing method requires absolutely no effort, why is it not the number 1 option on your list?

  4. I am doing this fermenting process for 4 kinds of seeds brought home from Italy. Wont be going this winter to get more seeds.


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