How to Save Tomato Seeds - A Beginner's Guide

Saving your own tomato seeds is often the first rite of passage into the world of heirloom gardening. With nothing more than a ripe tomato, a few simple supplies, and a little know-how, you open the door to a dazzling array of tomatoes—striped, speckled, heart-shaped, pear-shaped, and every color from deep purple to sunny yellow. The best part? Once you’ve saved a variety, you’ll have it forever. Each season you’ll grow, harvest, and save again, gradually building a collection that can be passed down for generations.

That’s how my own journey began. What started as a handful of seeds soon turned into hundreds of varieties—not just tomatoes, but other garden favorites too. I found myself sharing them with family, trading with friends, and before long, I had slipped down the happy slope that eventually led to starting my own seed business. Seed saving has a way of pulling you in like that: one tomato at a time, until you realize you’re not just gardening anymore—you’re preserving history.

Heirlooms like these Mule Team tomatoes would be lost to history were it not for dedicated seed savers who brought them back from the brink of extinction.

Choosing the Right Tomato

Alright, let's get down to business.  I’m going to assume you landed here looking for a step-by-step guide on saving tomato seeds. Maybe you’ve got an heirloom in your hand, or maybe not—and that’s okay. What matters most is that the tomato you’re saving from is open-pollinated—in plain terms, not a hybrid.

Hybrids are created by crossing two different tomato varieties. The payoff is often higher yields and very uniform fruit, but the downside is that hybrids don’t grow true from seed. If you save seeds from a hybrid, the plants you get next year will be unpredictable—a genetic grab bag of traits that look nothing like the tomato you started with.

So how do you know what you’ve got? Check the tag—hybrids usually come with a higher price tag, so growers and seed companies are quick to label them. Look for the word 'hybrid' or alternatively 'F1', the industry term for hybrid.  Random fact: the 'F' there comes from the Latin word filial, or son of.  So, the F1 is quite literally the child of the first mating. Future generations are labeled F2, F3, and so on. Tuck that nugget away—you’ll thank me when you start dabbling in tomato breeding. Like I said… slippery slope.

As we will soon learn, the flower (and coincidentally, foliage type) play important roles in determining the outcrossing frequency of a particular variety.

Isolation Distances

I know, you've got a tomato in your hand, probably already cut open, and you're like "Isolation Distances—what?" Don't worry, for the purposes of most gardeners, isolation distances aren't all that important.  Just know that with tomatoes there is a small possibility of outcrossing—that is, a small chance that the tomato you're holding was spawned by a little rendezvous with the neighbor's tomato or possibly another tomato in your garden (this event, of course, must be facilitated by bees as tomatoes don't have legs). Again, it's unlikely, but if you want to be sure that it doesn't happen, you can space plants generously—at least 3-5 feet apart—or use blossom bags.  If you want to learn more about this, read on.  If you want to get to squishin', skip down to the Step-by-Step Guide.

Tomato Pollination

First, some basic biology: tomato flowers are perfect—they contain both male and female organs within the same flower.  Typically, pollination occurs inside the flower through the normal course of development.  The female part, the stigma, contacts the male parts (pollen-containing anthers) leading to fertilization and seed development. 

Rarely, however, a variety may have exerted stigmas that extend outside of the flower.  This exposes them to pollination by insects, opening up the possibility that they may be "outcrossed" by a different variety.

Varieties most likely to have exerted stigmas include potato-leaved varieties like Brandywine Pink, Brandywine Red, and Hillbilly Potato Leaf, as well as currant tomatoes like Everglades and Texas Tiny.  To ensure total purity, these varieties must be separated by 1/4 mile or bagged.

Potato-leaved varieties like Hillbilly produce higher proportions of outcrossed seeds, owing to their exerted stigmas.

Step-by-Step Guide to Saving Tomato Seeds

Alright with all the basics covered, we're almost ready to squeeze some tomatoes.  In the following sections, I've laid out some basic steps that will get you well on your way to saving your own tomato seeds.  Let's get started!

Selecting the Fruit

Select tomatoes that are healthy and uniform.  They should not have any obvious signs of disease, and the fruit shape should be true-to-type for that variety.  Avoid selecting double-fruit—those that appear to be fused—as the large flowers that give rise to them are more likely to outcross.  Also avoid using the first fruit of the season as the limited number of flowers present at that time of year increases the odds of outcrossing.

Finally, and this point is most important, select fruit that are fully ripe.  You want the seeds to reach full maturity before you remove them from the fruit.  Under-ripened fruit will yield seeds with poor germination potential.

It's best to save seeds from multiple fruit of the same variety.  In the event that a cross-pollination or random mutation did occur, it would likely only affect one fruit.  Saving seed from multiple fruit, therefore, ensures that you have some good seeds to select from next year.

These uniform, healthy, and fully ripe Marglobe tomatoes are ready to be squeezed.  Saving seeds from multiple tomatoes and/or plants will ensure that diversity is preserved while minimizing the effects of potential outcrosses.

Fermenting Tomato Seeds

First of all, why should you ferment?  Most of us, at some point, have scooped seeds off the cutting board and smeared them onto a paper towel—and that works, at least to some extent.  But fermentation offers a lot of benefits:

• It improves germination. Tomato seeds are covered in a gelatinous coat that inhibits germination. Fermentation degrades this coating, thus improving the sprouting frequency and time to emergence.
• It reduces seedborne diseases like bacterial canker which can cause blotchy lesions to occur on the stems and fruit of plants.
• It produces clean seed.  Once dry, the seed will be clean in appearance and smell.  And it can easily be separated.  No more peeling dirty seeds off of paper towels, yay!

Fermenting tomato seeds releases their gelatinous coat and minimizes disease, yielding clean, high germinating seed.

Preparing Your Containers

Before we make a mess, let's get some containers ready.  I've found that canning jars work best, but I've seen others use deli or cottage cheese containers.  It really doesn't matter too much. Whatever you use, be sure to label the container with the variety you're extracting.

How to Ferment

1. Now we're ready to squish.  Cut the tomato in half to expose the locules (the juicy cavities inside the tomato).  You should have the stem side in one hand and the bottom of the tomato in the other.
2. Squeeze the juice and seeds into a container. Work your hands around the tomato to release all the seeds.  The bottom half should release its seeds easily. The top may require a little more manipulation.
3. Cover jar with fine mesh.  Pantyhose work well, but who has those anymore?  I use mesh drawstring bags that I bought on Amazon.  The exact material doesn't matter, but it needs to be porous.  Fermentation requires oxygen.
4. Secure mesh with rubber band or canning jar band (screwed right over the mesh). Fermentation is a stinky process that attracts fruit flies.  You don't want them getting in there or you'll have gross, wiggly things in your seeds.
5. Wait.  Put the seeds somewhere warm.  Fermentation occurs most efficiently at 72-80 degrees F.  Under these temps it should take 2-3 days.  Lower temps will require a longer fermentation period.
6. Watch.  Look for bubbles emerging from the mash.  With time, a fuzzy white film will cover the top of the liquid.  That's a good sign.

Fermentation is complete when a thick film of bumpy white fungus covers the top of the mash.

Cleaning the Seeds

Alright, you've got a stinky jar full of muck covered in a bumpy, white film and your roommate, partner, spouse is asking when you're going to deal with it.  It's time to wash.  First, get your supplies ready.  You're going to need a strainer/colander, a coffee filter, and a paper plate labeled with the variety name (use a permanent marker).

1. Stir vigorously.  You want to separate the seeds from the pulp.  The fermentation has done it's job, but the seeds are still suspended in the thicker muck.  You need to help them break free. A whisk or fork works well here.  You want to really whip it.
2. Let the seeds settle.  Good seeds will sink. Give them a few seconds and you should see them settling on the bottom.
3. Add water.  Pour off the muck on top if you need to make room.  If you've stirred well, that should just be pulp and unviable seed.
4. Stir vigorously. Now you should have tomato-tinted water with some chunks still in it.  Whisk it good again to break more of the gunk free.
5. Let the seeds settle.  Seeing a trend here?  Yep, this is basically the game.  Pour off the icky water.
6. Repeat. Keep filling with clean water, stirring, settling, and pouring off until you have clean seeds on the bottom and clean water in the jar. This process is called decanting.
7. Prepare your colander.  Put the coffee filter in the colander.  Dump off most, but not all of the water.  The seeds should still be in the bottom of the jar.
8. Swirl.  Give the seeds and remaining water a good swirl.  They want to sink so you'll need to keep them suspended so they'll pour out of the jar.
9. Pour seeds onto the coffee filter.  Be careful not to let the seeds spill over the sides of the filter.  Add a little clean water back to the jar to get the remaining seeds that are clinging to the sides.  Swirl and pour again.
10. Move to a paper plate.  Tilt the colander sideways and carefully pull the coffee filter containing the seeds onto the paper plate.  The plate adds structure and helps wick water away from the seeds so that it can evaporate more quickly.

Stages of tomato cleaning. Top left: Tomato seeds sinking to the bottom after being stirred. Top right: The same seeds after a few washes. Bottom left: Straining the clean seeds. Bottom right: Drying the seeds. A paper towel is placed under the seeds to wick water away from the seeds. Alternatively, a paper plate may be used.

Voila!  There you have it.  If you'd like, you can spread the seeds into a thinner layer so that they'll dry more quickly, but it's not necessary.  Keep them in a warm, well-ventilated room until completely dry.

Storing Tomato Seeds

I like to give my seeds a full week to completely dry.  It's probably overkill, but I've put quite a bit of work in by this point—I don't want to lose them to mold.  Once they're completely dry, I peel the seed "disc" from the coffee filter (this is my favorite part) and rub it between my hands to separate the seeds.

Tomato seeds should be stored in an airtight container.  Jars work fine, as do Ziplock bags.  If you're a Thresh Seed Co. customer, you probably have some of our resealable, mylar-lined packets lying around that just happen to be perfect for storing your own saved seeds (wink, wink).

Be sure to label the jar, envelope, etc. with the variety and date.  Tomato seeds will remain viable for 5-10 years when stored properly in a dry, dark place with consistent temperature (68 to 72 degrees is fine).

A Note on the Water Question

Now that you're familiar with the process of harvesting tomato seeds, I can bring up a common point of debate among seed saving enthusiasts: adding water to the tomato mash prior to fermentation.

Some people like to add water, particularly to dry, paste varieties like San Marzano or Martino's Roma.  We avoid adding water whenever possible.  My view is that nature is pret-ty good at figuring these things out and I don't want to mess with that chemistry.  Instead, I get a little more aggressive when squeezing the fruit, releasing more juice so that the seeds are entirely covered with juice and pulp.

Saving tomato seeds is a stinky process, but the result is well worth it.  Just look at this 1884 tomato! Once unavailable commercially, you can ensure you'll always have it by saving your own seeds.

Conclusions

Well, there you have it.  Before long, you'll be a veritable expert in tomato seed saving, amassing your own seed collection and sharing it with others.  Enjoy the messy, stinky process, because the reward—a world of colorful heirlooms, all at your fingertips—is worth it.

Want to get started today?  We offer over a hundred of the rarest, most flavorful heirloom tomatoes available, all trialed and true for flavor, uniqueness and outstanding garden performance.  Find your new favorite today!