How to Save Tomato Seeds the Right Way From Start to Finish

You’ve put all the work into learning how to grow tomatoes and how to prune tomato plants, maybe even building DIY tomato cages and waging war against tomato hornworms, all so that you can enjoy the amazing, fresh flavors of your favorite tomato plant varieties. Now the final step is ensuring that you can continue enjoying them for many more seasons to come through seed saving.

That is the whole spirit of seed saving—taking seeds from the crops that you enjoyed, that tasted good, produced well, or had some favorable attribute you think is worthy of continuing on in future years and preserving them. 

Saving tomato seeds is a little different than saving seeds from other crops because they have a protective gel coating that needs to be removed before storage. So here’s how to save tomato seeds like a pro, including how to harvest fresh seeds, fermentation of tomato seeds to remove gel, and how to dry tomato seeds so they are ready to store.

Product Spotlight

What Goes Into a Seed Packet

Many people who buy seed packets don’t understand all the work that goes into producing the seeds for that packet. From starting seeds and transplanting seedlings to maintaining plants, preventing cross pollination, harvesting the fruit, and processing the seeds, there’s a lot that goes into every packet! 

It’s a labor of love that you can learn how to do on a smaller scale at home with my Complete Guide to Seed Saving, along with crop-specific guides on how to save pumpkin seeds for planting, how to save bean seeds, how to save lettuce seeds, and how to harvest sunflower seeds to save.

Choosing the Best Tomatoes for Seed Saving

When saving tomato seeds, I always recommend selecting the healthiest, most productive plants with characteristics that you want to preserve. In the video, I demonstrated saving seeds from a new variety called Bountilicious tomato. Just one of our Bountilicious plants produced over 100 tomatoes with great flavor, excellent acidity, and very little disease.

Those are exactly the kinds of characteristics that I look for when choosing plants for seed saving. By saving from the best plants, strong genetics and desirable traits will be passed on to future generations.

Bagging Blossoms

If you’re saving seeds from heirloom tomatoes and want them to grow true to type, avoiding cross pollination is a must! That’s why the first task to be done for saving tomato seeds is bagging blossoms.

Tomatoes have perfect flowers, meaning that the male and female reproductive parts are contained within the same flower and they are primarily self-pollinating. But insects can still transfer pollen between varieties, which will create seeds that grow fruit different from the mother plant.

To prevent cross pollination, we use organza blossom bags to cover flower clusters before they open! These bags block insects from carrying pollen between varieties while still allowing the flowers to self-pollinate.

Pro-Tip: If you’ve had problems with tomato plant flowers dropping and poor fruit set, hand pollinating the flowers inside the blossom bags can increase fruit set by up to 50%! All you have to do to hand-pollinate tomato flowers is tap the top of each flower for about 5 to 7 seconds. This mimics a bee or wind, causing vibrations that drop the pollen from the male portion of the flower down into the female portion of the flower. 

Once fruit sets, remove the bags because the tomatoes can no longer be cross pollinated. Make sure you mark the tomatoes you used blossom bags on in some way so you can identify which ones to harvest for seed saving. (Try loosely tying bright colored yarn at the base of those flower clusters.)

If you don’t want to use blossom bags, you can isolate different tomato varieties by distance, spacing varieties a minimum of 100 to 150 feet apart to prevent cross pollination. However, blossom bags are an easy, inexpensive way to protect individual flower clusters without needing a large growing area. Remember, you don’t need to bag all your blossoms. Just one tomato can provide enough seeds to grow dozens of plants!

When to Harvest Tomatoes for Seed Saving

I recommend allowing tomatoes to reach peak ripeness on the vine, even if that means leaving them a little longer than you would for fresh eating. Some of the tomatoes we harvest for seed saving are actually past the point when I would prefer to eat them, but that’s okay because the goal is to allow the seeds inside to reach full maturity, giving them the best chance of germination next season.

Why You Need to Ferment Tomato Seeds

Unlike most vegetable seeds, cucumber, melon, and tomato seeds are surrounded by a slippery gel coating. This coating makes it very challenging to save the seeds effectively. 

Seeds like this are better off being fermented before saving because you have a much better end product. This is accomplished by soaking them in water for 4 to 5 days, during which the gel and any other plant material will rise to the top and break down while the viable seeds sink to the bottom.

Supplies Needed

Most of the supplies needed to save tomato seeds are probably already in your kitchen.

• Mature Tomatoes - Wait until the fruit is at near-peak ripeness before harvesting it. This is important because the seeds inside an immature tomato may not be fully developed or viable. 

• Kitchen Knife - Grab a sharp kitchen knife to cut the tomatoes with. 

• Cutting Board - Any kitchen cutting board or flexible cutting mat will work. 

• Bucket - A clean 5-gallon bucket works well, especially if you are saving tomato seeds on a larger scale. You can also use mason jars for fermenting seeds. If you have a problem with fruit flies, you can get fermenting lids that fit mason jars to keep them away. 

• Water - Regular tap water is all you will need.

• Potato Masher - A cheap potato masher is optional, but helpful.

• Strainer - I like to use a fine mesh strainer to separate the seeds out of the water after fermentation.

• Wax Paper - Use wax paper or parchment paper to dry the seeds on.

• Seed Saver Packets - Seed saver packets will keep your seeds organized and protected. 

How to Save Tomato Seeds

After harvesting your tomatoes, follow these steps to save the seeds:

1. Slice Open Tomatoes - Using the kitchen knife and the cutting mat, slice open the tomatoes across the equator, rather than from stem to blossom end. This cut exposes the seed cavities, making it much easier to get all the seeds out.

2. Squeeze Out Seeds - Squeeze the tomato halves like a lemon and gently shake if necessary, letting the seeds and gel fall into a container like a mason jar or bucket. If you have multiple tomatoes, you can continue putting seeds of the same variety into the container until it is is about ⅓ full.

3. Add Water - Add water to the container at a ratio of about 1 or 1 1/2 parts water to 1 part tomato seeds/gel. Do not exceed 2 parts water to 1 part tomato mixture. For myself, I prefer to keep the ratio close to 1:1, adding one cup of water to every one cup of tomato seeds/gel.

4. Ferment - Place the container in a location away from living areas (because the mixture will develop an unpleasant odor) like a garage or utility room and leave it to ferment for 3 to 5 days. Don’t be alarmed if some mold develops on the surface. Pro-Tip: Ferment for 3 days at the very minimum, 4 days is usually ideal, or maybe even 5 days if it is in a cooler location, but no longer. Over-fermenting will start to break down the seeds themselves.

5. Separate the Seeds - Use the potato masher or a similar tool to gently break up the mold layer and any thick parts of the fermented seed mixture. (If you used a mason jar, you will likely need to pour the fermented seed mixture into a bucket or other container at this time.) 

6. Clean the Seeds - Fill the bucket or container with clean water. Allow the seeds to settle to the bottom by waiting about 15 seconds. Then slowly pour off the dirty water, taking care not to dump out the seeds with it. Repeat this step 2 or 3 more times until the seeds are clean.

7. Strain Out Seeds - Pour the seeds into a fine-mesh strainer to remove the rest of the water. You can gently press on the seeds in the strainer to get out even more water.

8. Put Onto Wax Paper - Write the tomato variety on a sheet of wax paper and put the seeds on the wax paper to dry. Spread out clumps into a single layer as much as you can so all the seeds get good air flow to prevent mold or premature germination.

9. Dry Seeds Thoroughly - Leave the seeds to dry on the wax paper in a location that is well-ventilated where they will be unbothered for about 2-3 weeks. Even if they appear dry earlier, let them continue to dry a full 2-3 weeks. 

10. Package & Store Seeds - Once completely dry, gently rub any clumps of seeds between your fingers to separate individual seeds. Put the seeds in seed saver packets and label them with the variety name and harvest year before different batches can get mixed up! Store your seed packets in seed storage containers in a cool, dark, dry location to maintain seed viability.