How to Save Tomato Seeds: The Fermentation Method, Step by Step

You grew a tomato this summer that was better than any you can buy: the right size, the right sweetness, perfect for your garden. The good news is that you don’t have to hope you’ll find it again. You can save its seeds in a few days with nothing more than a jar and some water.

Tomatoes are one of the best crops for a first try at seed saving. Here’s how to do it properly.

Before you start: is your tomato worth saving?

Check that it isn’t a hybrid. If the variety is labelled “F1”, its seeds won’t grow plants like the parent. Heirloom and open-pollinated varieties such as ‘Brandywine’, ‘San Marzano’, ‘Black Krim’ or ‘Gardener’s Delight’ will come true.

Pick the right plant. Choose a healthy plant without leaf spots or wilting, one that gave you good fruit. Seed from a sick plant can carry some diseases into next year.

Pick the right fruit. Let the tomato ripen fully on the vine. It should be deeply coloured and a little soft, even slightly past the point where you’d eat it. Seeds from a fruit picked green are less mature and may sprout poorly.

Tomatoes mostly pollinate themselves, so different varieties growing next to each other rarely cross. Some old varieties and currant tomatoes have flowers that bees can reach more easily. If you’re saving seed from those, a few metres between varieties is a good idea.

Why ferment tomato seeds?

Each tomato seed sits inside a small bag of gel. The gel stops the seed from sprouting inside the fruit. If you just scrape seeds onto a plate and dry them, the gel dries onto them like glue. They’ll often still grow, but they clump together and germinate less evenly.

Fermentation copies what happens in nature, when a fallen tomato rots on the ground:

• it breaks down the gel, so the seeds come out clean and separate;
• it helps separate good seeds from empty ones;
• it may reduce some seed-borne diseases on the seed coat.

It sounds complicated, but it’s really just leaving a jar on the counter for a few days.

What you’ll need

• 1–3 ripe tomatoes of one variety
• a small glass jar or cup
• water
• a sieve with fine mesh
• a ceramic plate, or a coffee filter
• a pen and a label (this matters more than you think)

Step 1: Scoop out the seeds

Cut the tomato across its middle, like a wheel, not from top to bottom. This opens up the seed chambers. Squeeze or scoop the seeds and gel into the jar. The rest of the tomato is still perfectly good to eat.

Add about the same amount of water as you have seed pulp. Label the jar immediately with the variety name. If you’re fermenting several varieties at once, they will look exactly the same in two days.

Step 2: Let it ferment for 2–4 days

Cover the jar loosely with a paper towel, a coffee filter or a lid set on top without screwing it down. Air should get in and fruit flies should stay out. Put it somewhere warm, out of direct sun. A kitchen shelf is fine. Stir once a day.

What you’ll see:

• Day 1–2: the mixture starts to smell sour, and some bubbles appear.
• Day 2–3: a layer of white or greyish mould forms on top. This is normal and exactly what you want.
• Day 3–4: the good seeds have sunk to the bottom, and the gel has broken down.

Yes, it smells. Put it somewhere you won’t mind for a few days, like a garage shelf or a utility room.

Don’t leave it too long. In warm weather, two or three days is often enough. After about five days the seeds may start to sprout in the jar. When most seeds are at the bottom and the mould layer is formed, move on.

Step 3: Rinse and separate

Fill the jar with water and stir. Let it settle for a few seconds. Healthy, heavy seeds sink. Mould, pulp and empty seeds float. Carefully pour off the top layer. Repeat this two or three times until the water is mostly clear.

Then tip the seeds into the sieve and rinse them under the tap, rubbing gently with your fingers. Clean seeds feel slightly fuzzy, not slimy.

Step 4: Dry the seeds

Shake off as much water as you can, then spread the seeds in a thin layer on a ceramic plate or a coffee filter.

Avoid paper towels. Wet tomato seeds stick to them, and you’ll end up peeling them off one by one or planting bits of paper next spring.

Leave them somewhere airy at room temperature for one to two weeks. Break up the clumps with your fingers every day or two so every seed dries evenly. Keep them out of direct sun and away from radiators or ovens. High heat can damage seeds.

The seeds are dry when they’re loose and feel crisp, and none of them stick together.

Step 5: Pack and label

Put the dry seeds in a paper envelope or seed packet and write down:

• variety name;
• year harvested;
• anything useful: “earliest plant”, “great for sauce”, “from Grandma’s garden”.

You can make a nice-looking packet for free with the Seed & Share packet maker, print it at home and fold it in a minute.

Stored cool, dark and dry, tomato seeds stay good for four to six years or even longer. See How to Store Seeds So They Last for Years for the details.

The quick version (no fermentation)

Short on time? You can skip the fermentation:

1. Squeeze the seeds into a sieve.
2. Rinse them under running water, rubbing to get off as much gel as possible.
3. Spread them on a plate and dry as above.

These seeds usually germinate fine. They just tend to stick together and are a little less clean. For a few seeds for yourself, it works. For seed you plan to share or keep for years, fermenting is worth the extra few days.

Common questions

Can I save seeds from a supermarket tomato? You can try, but most supermarket tomatoes are F1 hybrids, so you won’t know what you’ll get. Heirloom tomatoes from a farmers’ market are a better bet.

How many seeds will one tomato give me? Usually from 50 to over 200, depending on the variety. One fruit is more than enough for your own garden, with plenty left to share.

The mould looks scary. Did I ruin it? No. A layer of mould on top is a sign that fermentation is working. It rinses off with the floating pulp.

Some seeds sprouted in the jar. What now? They fermented too long or too warm. Throw out the sprouted ones and dry the rest. Next time, check after two days.

One tomato, a hundred gifts

Just one good tomato can give you seed for years, plus enough to share with every gardener on your street. Pack a few envelopes, write the story of the variety on the back, and pass them on. That’s how heirloom tomatoes became heirlooms in the first place.