Harvesting seeds from the garden is not the end of the seed saving process, because most seeds come along with fluffy, bristly chaff, or gooey pulp - all the remnants of the flowers and fruit where the seeds grew. A lot of the time you can get away without perfectly cleaning your seeds, especially if you're only saving a small amount for your own use. On the other hand, if you offer seeds to other gardeners they'll probably expect them to look like the nicely-separated seeds we're all used to seeing in packets. Also, the pulp and chaff around your seeds can absorb moisture from the air, and sometimes cause mouldy problems for the seeds in storage. Moreover, the most pressing reason might be that your seeds will take a lot less space when they're freed from the other stuff.

There are three main categories of seeds when it comes time to clean them: seeds that grow in wet fruit, seeds that grow in pods, and seeds that grow in fluffy or fragile seed heads.

Wet-fruited Seeds - Use Water

Tomatoes, peppers, eggplants, and melons are some examples of seeds that ripen inside a wet fruit. Usually the seeds are ripe when the fruit is fully ripe (not so with cucumbers though), and the fruit should ripen on the plant to give maximum nutrition to the seeds inside them. Carefully slice the fruit open, and scoop out the seeds, rinse with water, and let the seeds dry fully before storing them in breathable paper envelopes or bags.

You can imagine how simple this is for peppers and cantaloupe melons, but it's trickier with some fruits like tomatoes or squash. Every tomato seed is encased in a sac of jelly, which makes the seeds hard to pick up with your fingers. It also helps keep the seed dormant, so it doesn't germinate too early. That means, if you don't clean off that jelly your tomato seeds will be stubborn to sprout in spring. Also, the jelly will dry but even then it tends to absorb moisture from the air and it can make your seeds mouldy in storage.

If you are only saving a few tomato seeds, you can just rub off the jelly with your fingers or a cloth. Then let them dry. If you're saving many tomato seeds, it's easier to put them in a closed container at room temperature for 3 days, then rinse the rotten pulp through a sieve. It doesn't smell good, but the seeds come out nice and clean.

Read more about saving tomato seeds with our three-part series: 

With squash, the secret to freeing the seeds from the stringy pulp is to scoop them into a bucket of water, and rub them with your fingers until the strings separate.  

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Podded Seeds - Use Air and/or Screens

Beans, peas, other legumes like chick peas, brassicas, and some garden flowers like larkspur grow in pods. The pods should always be allowed to mature to their dry, brown stage while on the plants. That makes sure the seeds are fed as much as possible, so they will store longer. It's okay to leave the seeds in the pods for awhile, even until spring, but make sure they're open to the air and any excess moisture can escape. Otherwise, the pods and seeds will mould.

You can easily remove the seeds by breaking pods open with your fingers, and that's the best way if you're only saving a few seeds. For larger amounts, you'll soon find that it takes a lot of time. It's much faster to let the pods dry really well until they get brittle, then crush them in a large container so they shatter open and drop their seeds. You can use your foot, a 2x4, or anything, and if the seeds are really well dried they won't be damaged.

Then sift the empty pods off the top, and you'll find your seeds at the bottom of the container. A screen, or a light breeze from a fan can help separate the dust and the last bits of broken pods, and you'll have nice clean seeds to share with other gardeners.

Seed Heads - Use Air and/or Screens

Lettuce, most herbs, grains, and almost every garden flower grow their seeds in "heads" that turn brown when the seeds are ripe. Normally, you should let the seeds ripen fully on the plants, and gather them by picking the seed heads into a bag or container that can breathe and allow moisture to escape. As the seed heads dry out, they often drop their seeds, and they become fragile so you can separate the seeds from their heads just by squeezing and rubbing with your fingers.

These are among the most challenging seeds for home seed savers, because the chaff is difficult to separate from the seeds, and the process makes a lot of dust. We normally like to get rid of the dust first, by sifting the seeds and chaff through a fine screen, small enough to keep the seeds but allowing the dust to float away. A light breeze from a fan helps, and it's probably a good idea to do this outdoors.

Once the dust is gone, you can work with different sizes of screens to find one that allows the seeds through, but not the larger pieces of stems, leaves and flower parts. Also, try to find a screen that's just barely fine enough to keep the seeds, but allows the smaller bits of chaff to fall through. Not only do you wind up with seeds that are much cleaner but you will probably have also removed the thin, unpollinated seeds that didn't form properly. Those would not have sprouted, so you will have actually increased the germination rate of your seeds!

Finally, a light breeze from an electric fan can really help. The seeds are usually the most dense objects in the seed heads, so almost all the other material will blow away before they do. Try putting the seeds and chaff on a shallow tray, with a fan some distance away. Gradually move the fan closer, and sift the seeds with your fingers so the finer, lighter chaff lifts up and blows off the tray. Be careful, and patient, so you don't blow your seeds away too! 

Learn more about saving seeds, and how to clean each species in our handbook "How to Save Your Own Seeds".

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Bob Wildfong is Seeds of Diversity's executive director