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Tomato Seed Saving - Complete Guide to Heirloom Tomato Seed Saving from Ethos Seed Company

Tomato Seed Saving - The Complete Guide

Now that summer is winding down, many gardeners find themselves wishing to save seeds from their own tomato plants. Tomatoes are such a beloved staple that many dub them the “Queen of the Garden”, and for good reason! Tomatoes  are one of the most commonly grown vegetable across the world. With over 3,000 varieties of heirloom tomatoes documented by experts like Craig LeHoullier, author of the 2019 book “Epic Tomatoes”, tomatoes have a lot to offer the gardening enthusiast. Some might even say that no single gardener can ever hope to grow them all.

But one can certainly try! Over my years of gardening, I grew hundreds of different varieties of heirloom tomatoes with varying degrees of success, leading me further and further into what enthusiasts dub the “tomato craze”. Before I realized it, I had dozens of seed packets, notebooks full of handwritten notes and computer folders brimming with hundreds of pictures!

Dr. Wyche Yellow heirloom tomato - a cherished variety worth saving for future generations

Dr. Wyche Yellow heirloom tomato - a cherished variety worth saving for future generations

Whether they decide to grow a few select varieties of cherished heirlooms year after year or dive into the crazy world of tomato breeding, most gardeners find themselves wishing they could save their own tomato seeds at some point or another on their gardening journey. The reasons for wanting to harvest and preserve one’s own seeds are varied, from the difficulty to source some rare heirlooms to the fickleness of the large seed companies who may drop a favorite variety without a warning.

Owning one’s own seed supply is a safeguard against uncertainty and a guarantee that the precious, delicious tomatoes from yesteryears find themselves growing again in the gardens of the future.


Selecting Plants

Seed saving starts by selecting plants that display the characteristic worthy of preservation for future generation. Gardeners should always save seeds from the plants showing the best traits of their chosen varieties as well as vigor, high yield and disease resistance. Those can be hard to quantify, and it can be harder still to find plants that display all the desirable characteristics at once, so proceeding by elimination can be a timesaving and sanity-preserving process!

Simply start by eliminating the plants that show disease susceptibility, low yield and stunted growth. As a general rule, I find it best to wait until the end of the season to pick fruits destined for seed preservation as it gives a better overall idea of the plant’s yield and vigor. This is also the best way to select for disease resistance as you will know which plants have succumbed early to plagues like bacterial blight. A gradual selection for vigor by the gardener will give long lasting results that may end up giving you a definite improvement over the seed line purchased from the store.

The next step will be to save seeds from plants that produce fruits that are consistent with your chosen variety. Read the description of your variety and pay close attention to things such as skin color, flesh color (or colors!), shape and size, fruiting arrangement and of course, taste. Those are the characteristics that have been developed and selected by generations of gardeners before and should be preserved to respect the authenticity of the variety. This is what an heirloom is all about, after all!

Sunshine Bumblebee Cherry tomatoes displaying proper variety characteristics from Ethos Seed Company
This Sunshine Bumblebee Cherry tomato plant displays high yield, vigor and proper fruiting characteristics. It is a good choice for seed harvest.


When making your selection, don’t forget one thing: you are preserving the genetic material of the plant, not the individual fruit you are collecting. Keep this in mind when making your decision, as well as the timing of your decision. Large beefsteak tomatoes tend to have smaller fruits at the beginning of the season, so don’t judge the plant negatively for it. Instead, keep records of fruit sizes, taste and color for the entire plant before preserving its genetic material.


Maintaining your variety

Tomatoes, or Solanum Lycopersicum, are inbreeding plants that produce perfect flowers fully capable of self-fertilization without the presence of a pollinator. They do not experience inbreeding depression and seed lines can be preserved indefinitely without hurting yield or vigor. This means that in a perfect world, each tomato plant produces perfectly pure seeds shielded from cross-pollination.

But..... if you are reading this article and have been gardening for a while, you know that the world isn’t perfect and that nature always finds a way!

In fact, considerable controversy exists around the subject of tomato crossing. According to expert seed saver Suzanne Ashworth in her 2002 renowned book “Seed to Seed”, tomatoes do experience varying levels of crossing. The anatomy of the flower plays a large role in the amount or absence of crossing of a variety.

Tomato Flower Anatomy - for heirloom seed saving - Ethos Seed Company

Tomato flower anatomy - note the fused Stamen and the retracted style. In some tomato flowers, the style protrudes past the stamen and is exposed to potential pollinator visits, increasing the chances for cross-pollination.


For example, according to Ashworth, all potato leaf varieties have protruding styles, which exposes the receptive female part of the flower to outside pollen. Double blossoms, which are common in large beefsteak types of tomatoes, also have exposed stigmas, making them prone to insect cross-pollination.

To determine the type of bloom of a particular variety, the gardener should examine a sample of flowers from each plant under a magnifying glass. It should be noted that most available heirlooms of cherry, paste, slicing and beefsteak tomatoes have retracted styles (apart from the double blossoms on beefsteaks) and should be safe to use for variety preservation.

Tomato flower with fully retracted style - perfect for self-pollination and representing little risk of cross-pollination

Tomato flower with fully retracted style from a Chadwick Cherry Tomato - perfect for self-pollination and representing little risk of cross-pollination


Tomato flower with protruding style on potato leaf variety- representing high risk of cross-pollination

Tomato flower with protruding style on potato leaf variety- representing high risk of cross-pollination

Tomato flower with with double blossom on a Black Krim tomato plant- representing high risk of cross-pollination

Tomato flower with with double blossom on a Black Krim tomato plant- representing high risk of cross-pollination


If the tomato variety you want to preserve have a protruding style, then blossom bagging will be necessary to isolate the blooms. This is an easy technique and does not require much in terms of financial investment or fancy equipment. A simple, inexpensive spun-polyester bag is placed over the flower cluster until all the blooms have faded and the fruits are starting to form. The bag can then be removed, and the flower cluster marked with a piece of string. Those seeds will be perfectly pure for variety preservation. Those little bags can be reused many times over a season!

Proper Tomato Ripening

Harvesting seeds differs from harvesting a tomato for the table. Most gardeners harvest large beefsteak tomatoes as soon as they blush to protect them from critters and other nuisance, preferring to allow them to ripen in the safety of an indoor location.


German Pink Tomato - a shy seed producer with exceptional taste, yield and disease resistance, fully ripe on the vine
German Pink Tomato - a shy seed producer with exceptional taste, yield and disease resistance, fully ripe on the vine. This is an excellent example of a variety where every seed counts!


This is not an optimal choice when it comes to seed saving. Tomatoes chosen and harvested for the purpose of seed saving should be very ripe, almost past their edible stage. The longer the seeds are allowed to mature on the plant, the most viable seeds will be collected. This is very important to know in the case off those heirlooms that produce few seeds, like paste tomatoes, where every seed may count!

So, allow the tomatoes to ripen fully on the vine, past the optimal stage if you want to increase the number of viable seeds present in any given fruit.


Processing the Seeds

Unlike dry seed saving as is the case for beans, peas or herbs like cilantro, tomatoes are wet seeds and need additional steps to produce viable seeds with an acceptable germination rate.

Each tomato seed is encased in a gelatinous sack that contains chemicals inhibit germination. This little trick of nature prevents the seeds from sprouting inside the flesh of the tomato. If left to its own device, the ripe tomato would fall from the plant and rots away during Fall and Winter, destroying the gel sack and allowing germination in the Spring when conditions for growth are optimal. This is a common strategy for plant survival.

Tomato seed encased in its gel sack

Tomato seed encased in its gel sack

The natural rotting process needs to be replicated for home seed saving purposes and it is quite easy to do with a process called fermentation. Fermentation is a natural phenomenon broadly defined as the process by which microorganisms bring about a desirable change in organic matter. In layman’s terms, microorganisms naturally present in the tomato and on the tomato skin will effectively digest the gel sack surrounding the seed, replicating the natural process of rotting in a short amount of time.

The resulting seeds can then be washed and dried for long term storage with a high germination rate.

Sounds good? Now how can you go about doing this?

It’s quite easy! Cut the tomato in half (or don’t in the case of cherry tomato, currant tomatoes and other small fruiting tomatoes) and press the gel and the seeds into a large glass container. Remove as much of the pulp as you can since it will simplify the cleaning process further on. I like to use a quart Mason jar and press the fruits over the opening to express the seeds ang gel, but the choice of the container is totally up to you. Continue until you have collected all the gel and seeds you want.

Jars of tomato seeds and water on windowsill, fermenting
Jars of tomato seeds and water on windowsill, fermenting


Next, fill the jar with room temperature water until the tomato seeds and gel float on the surface. It helps to mash things up with your fingers, but it’s not necessary.

Now, place the jar on a shelf away from direct sunlight and allow the natural fermentation process to occur. A few days later, the gel will be dissolved, the seeds will have fallen at the bottom of the jar and a thin layer of grey or white mold will cover the water surface. This is a smelly process and is best done outside, but care must be taken to prevent the container from drying up in high temperature.

As the mold layer covers the entire surface, it is time to stop the fermentation process.

Tomato seeds seeping at the bottom of jar after fermentation

Tomato seeds seeping at the bottom of jar after fermentation


To clean the newly fermented seeds, scoop out any plant matter floating at the surface as well as the layer of yeast and bacteria covering and discard – or even better, compost it! Next, pour the water out carefully, not allowing the seeds that are at the bottom to escape. It might be beneficial to use a strainer, but if you go slowly, you don’t have to.

Don’t fret about the floating seeds trying to escape. Those are lighter than the others because they lack the embryo making the seeds viable. The heavier seeds waiting at the bottom are the ones you want to keep.

Fill the jar again with water, agitate and pour. Repeat until your seeds are clean.



Drying is perhaps the most important part of the entire seed saving process and should be done immediately after the fermentation process. If not dried immediately, the seeds will germinate and your efforts will be wasted.

Simply lay your newly cleaned seeds on a flat surface to dry, away from direct sunlight. Do not make the mistake of laying your seeds on a paper towel to dry! The paper will be next to impossible to remove once the seeds have dried out. A ceramic or plastic plate is all it takes, but some people also like to use coffee filters.

Thoroughly dry heirloom tomato seeds
Thoroughly dry heirloom tomato seeds  


Stir the seeds every day, ideally twice a day, to prevent from clumping together.

The seeds must be completely dry before storage, so allow at least 2 weeks in a dry environment for drying up. Do not place the seeds in direct sunlight to prevent the embryos from being damaged by the heat and radiation from the sun.

To store your seeds, place them in a dry, cool, dark place, but not in an airtight container. Those dry seeds are in a dormant state and will continue to breathe slowly.

For the serious seed saver, a dehydrator is a must. Select one that allows for a heat setting of 95 degrees Fahrenheit and dry the seeds completely over the course of 12 to 24 hours. This will put the seeds into a deeper state of dormancy and allow you to store in a sealed container for long term storage or freezing. If frozen, those seeds should keep a decade or more, indefinitely, really. Be careful, though, when taking them out of the freezer: allow to thaw before opening the sealed container to prevent moisture from condensation from ruining them. 

Unless you use a dehydrator do not store your seeds in a sealed container such as a mylar bag. The normal humidity content present at room temperature is too high for long term storage such as this. Simple paper envelopes or Mason jars with a screwed lid work perfectly.


Seed Viability and Shelf Life

Tomato seeds have famously long shelf life! A span of 4 to 7 years is generally accepted under ideal storage conditions.

Simply store your seeds in a cool, dry place, away from light to keep the germination rate up. Alternatively, the thoroughly dried seeds can be frozen, further extending the shelf life to a decade or more.


Tomato Seeds Fact Sheets - Ethos Seed Company


What are your favorite heirloom tomato varieties? Do you save your own seeds from them, or do you rely on seed companies to provide them for you? Leave a comment below!

Tags: Seed School


  • Posted by Debbie Will on

    Black Vernissage Tomato is an heirloom tomato that has been chosen by me as best of the best. I received a package from a garden show in 2017 and started them by seed this year. Almost all of them germinated and have developed into a wonderful plant. They are very prolific and are extremely tasty. They are wonderful sliced or especially used in a caprese salad. I am looking forward to saving some of my own seeds this year.

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