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How to Save Tomato Seeds: The Fermenting Step

Tomato seeds need fermenting to remove the germination-blocking gel. Which varieties come true, the three-day process, and drying and storage.

By Zakaria 4 min read Save to Pinterest — opens Pinterest in a new tab
A tomato cut across the equator, showing seeds suspended in gel inside the chambers
Photo: Lee Ann Ratledge, CC BY 4.0, via Wikimedia Commons
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Tomato seeds arrive wrapped in a gel that stops them germinating. Removing it is a three-day job involving deliberate mould, and skipping it is why home-saved seed disappoints.

Check the variety first

What comes true, and what does not
TypeComes true?Examples
HeirloomYesBrandywine, Cherokee Purple, San Marzano, Black Krim
Open-pollinatedYesMoneymaker, Marglobe, Roma VF
F1 hybridNoSungold, Early Girl, Big Beef, most modern varieties
Supermarket fruitUsually notNearly all F1

An F1 hybrid is the first cross of two distinct parent lines. Its seed segregates in the next generation into a mix of grandparent traits, usually with worse fruit than either. The plants will grow; they will not be the tomato you liked.

Check the packet or label. “F1” or “hybrid” means do not bother.

Choose the fruit as carefully as the variety

Save from a healthy plant that performed well, not from the one fruit that happened to be left over. Take fully ripe — slightly past eating ripe is ideal — and from two or three different plants of the same variety if you have them, which keeps a little genetic diversity in the line.

Never save from a plant that showed disease. Several tomato diseases travel on seed.

Fermenting

  1. Cut the tomato across the equator and squeeze or scoop the seeds and gel into a jar
  2. Add a splash of water — roughly the same volume as the pulp
  3. Cover loosely with cloth or a lid set on top. It needs air, and it will smell
  4. Leave at room temperature for two to four days. Somewhere you are not eating
  5. Check from day two. It is ready when a white or grey mould layer covers the surface and it smells strongly sour
  6. Do not leave it past four days — seeds can start sprouting in the jar

The mould and the smell are the process, not a failure

It looks and smells like something has gone badly wrong. It has not. That surface mould is what digests the gel sac off the seed, and it kills several seed-borne bacterial diseases — bacterial canker and bacterial spot among them — which is why commercial seed producers ferment too.

The only real mistake is going too long.

Separating and rinsing

  1. Fill the jar with water and stir hard
  2. Wait a minute. Good seeds sink; pulp, mould and hollow non-viable seeds float
  3. Pour off the floating layer carefully
  4. Repeat three or four times until the water runs clear and only clean seed remains
  5. Tip into a fine sieve and rinse thoroughly under the tap
  6. Shake out as much water as you can and blot the underside of the sieve

The sink-or-float test is doing real work: the floaters are genuinely not viable, so this step improves your germination rate as well as cleaning the seed.

Drying

  • Spread in a single layer on a ceramic or glass plate, a coffee filter, or a fine screen
  • Never paper towel or kitchen roll. The seeds glue themselves to it permanently
  • Somewhere warm, airy, out of direct sun
  • Stir daily with a fingertip so they do not clump
  • One to two weeks, depending on humidity
  • Dry enough when they snap rather than bend

A fan in the room speeds it up. Heat does not — anything above about 95°F starts to damage viability, so no oven, no radiator, no sunny windowsill.

Storage

  • Paper envelope, labelled with variety and year, inside an airtight jar
  • A silica gel sachet in the jar if your climate is humid
  • Cool, dark, stable — a cupboard, or a fridge if it is genuinely dry
  • Four to six years of good viability, and often longer

Label as you go. Tomato seed all looks identical three months later, and a jar of unlabelled envelopes is a jar of unknown tomatoes.

Testing before you sow

Worth doing with seed more than a few years old:

  1. Ten seeds on a damp paper towel, folded into a plastic bag
  2. Somewhere warm — around 75°F
  3. Check after 5 to 10 days
  4. Eight sprouting means 80% germination. Sow normally
  5. Below about 50%, sow thickly or start again

It costs ten seeds and tells you whether to trust the packet before you commit a seed tray and three weeks of windowsill to it.

Common questions

How do you save tomato seeds?

Scoop the seeds and surrounding gel from a fully ripe tomato into a jar, add a splash of water, and leave it at room temperature for two to four days until a layer of mould forms on top. That fermentation dissolves the gel coating, which contains germination inhibitors. Then add water, stir, pour off the floating pulp and hollow seeds, and keep the good seeds that sink. Rinse them in a sieve, dry them on a ceramic plate for one to two weeks, and store somewhere cool and dark.

Do I have to ferment tomato seeds?

For reliable results, yes. Each seed is wrapped in a gel sac containing compounds that suppress germination — they stop seeds sprouting inside a rotting fruit — and fermentation is what removes it. Seeds dried with the gel still attached germinate erratically and store less well. Fermentation also kills several seed-borne bacterial diseases, including bacterial canker and spot, which is the second reason commercial seed producers do it.

Will seeds from my tomatoes grow the same variety?

Only if the plant was open-pollinated or an heirloom. Seeds from an F1 hybrid — anything labelled F1, and most modern supermarket and garden-centre varieties — do not come true: the next generation segregates into a mix of the grandparent traits, often with poorer fruit. Heirlooms such as Brandywine, Cherokee Purple, San Marzano and Moneymaker come true and are the ones worth saving. Check the packet or the plant label before you bother.

How do you dry and store tomato seeds?

Spread the rinsed seeds in a single layer on a ceramic or glass plate, a coffee filter or a fine screen — never on paper towel or kitchen roll, which they glue themselves to. Somewhere warm, airy and out of direct sun for one to two weeks, stirring daily so they do not clump. They are dry when they snap rather than bend. Store in a labelled paper envelope inside an airtight jar, somewhere cool and dark, and they stay viable for four to six years.

Can I save seeds from a supermarket tomato?

You can, and they will often germinate, but the result is usually disappointing. Nearly all supermarket tomatoes are F1 hybrids bred for shipping and shelf life rather than flavour, so the seedlings will not come true and what does grow tends to inherit the wrong half of the parentage. Some greenhouse varieties are also grown from seed treated to prevent resale. Start from a known open-pollinated variety instead.

Why did my fermenting jar go mouldy and smell terrible?

That is what is meant to happen. A white or grey mould forms on the surface and the mixture smells strongly sour within two or three days — that is the fermentation doing its work on the gel. What matters is stopping at the right point, because leaving it much beyond four days risks the seeds beginning to sprout in the jar. Check daily from day two, and move to the rinsing step as soon as the mould layer has covered the surface.

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