Cleaning Your Seeds: Separation & Winnowing Methods

Once you have harvested and fully dried your seeds you’ll need to separate the seeds from their pods or remove them from the seed heads, and then winnow them to remove bits of stems, shells, and other matter. Cleaning seeds is the final, rewarding step in the seed to garden to seed cycle.

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Separating Seed – Threshing

Threshing seeds involves rubbing, flailing, beating, or otherwise manhandling the seeds until they come loose from their pods or seed heads, but must be done without damaging the seeds. With a bit of practice, you’ll learn just how much pressure/force is needed, without using too much.

For three out of the four threshing methods described below, it’s easiest if the seeds are placed in a pillowcase or a cotton flour sack (aff link) before being worked on.

Threshing can be used for almost any type of seed that is harvested after it has dried on the plant, including legumes, members of the carrot family, most herbs, grasses, grains, etc.

Threshing methods

  1. Flailing
  2. Jogging
  3. Rubbing
  4. Beating
  5. Shaking/Tumbling


With the seed matter (the seed pods, seed heads, etc.) in a pillowcase or cotton flour sack (aff link), use a stick, broom handle, or walking stick to beat the seeds until they are released from the seed pods or seed heads.

A true flail is made up of two sticks, usually about the width of a thumb, with one about 2 ½ feet long and the other 1 ½ feet long, joined at one end with a leather strap or a chain. This tool made it easy to swing and hit the seeds.

Over time, a special box, called a threshing box, has been designed for holding the seeds while being threshed. It has sloping sides and is open at one end, allowing for easier threshing. It’s not necessary to use a threshing box, especially if you place the seeds in a pillowcase or cotton flour sack.


With the seed matter in a pillowcase or cotton flour sack (aff link), place the bag on a hard surface, and then lightly jog on them.

I have seen some seed savers recommend you wear tennis shoes when using this method, to help prevent crushing the seeds. From my personal experience, I have found that tennis shoes crush more seeds than if you jog on the bag barefoot, or wearing flip flops (to protect your feet from sharp bits of pods and seeds).

I also feel like I can gauge the amount of pressure needed to break seed pods more easily when I’m barefoot or wearing thin flip flops, than I do wearing tennis shoes.


Spread the seed matter on board, at least 2 or 3 feet wide. (A piece of plywood works well.) Use another board, a rolling pin, or a concrete floater, to crush the seed pods.

Another form of rubbing seeds free uses a mesh screen. Pour the seed matter on the screen and gently use your hand (preferably gloved) to rub the seed matter around the screen to release the seeds.


With the seed matter in a pillowcase or a cotton flour sack (aff link), bang the sack against something – the wall, the floor, the inside of a bucket, etc.

You can also do this while holding on to several stems at a time and beating the seed heads against the inside of a bucket, barrel, or trash can (clean, of course).


Shaking or tumbling is best used for seeds that are loosely attached to their seed heads, or for seeds in pods that have naturally split open.

Place the seeds in a small bucket with a lid, a Tupperware, a jar, or other close-able container. Seal the container, and then shake it or roll it vigorously to release the seeds.

Winnowing Seed

1. Moving Air

Moving air can be a very effective way to clean your seed and get rid of the chaff and other debris. It can also end up blowing away a lot of your seed with the chaff.

We’ve all seen videos of women with big baskets of wheat or other grains, tossing the grains into the air and using the natural power of the wind to winnow the seed. And it obviously works, which is why this technique has been used for centuries.

Wind speed and direction can be highly variable, and is likely to be stronger than you probably need. Using the wind to clean your seed will work well if there’s a significant difference in weight between your harvested seeds and the chaff you’re trying to get rid of. Grains are probably the best example – the grains seeds are dense, and the chaff is light and easily blown away.

Using small fans, a hair dryer without heat, one’s own breath, or a large fan set on a low setting or set back a ways from the winnowing area will all produce consistent force and direction, and is generally much milder than wind.

To use this method:

1. Lay out a sheet or tarp to cover the ground. If you choose to do it in your kitchen, you don’t necessarily have to do this, but it does make for easier cleanup.

2. Place a cookie sheet or a large baking tray on the ground, and place the fan so it will blow straight across it. (I prefer to use those large, catering steam pans. I use them over and over again for seed stuff.) (affiliate)

3. Pour the seed from 2 or 3 feet up, slowly, onto the baking tray. Repeat as necessary until seed is sufficiently clean.


This method will work best with seeds that weigh more than the chaff, even if the seeds themselves are still small. For tiny, lightweight seeds, this is not a very good method to use.

2. Roll & Fly

This method is best for seeds that are round like balls, such as those produced by the brassicas (cauliflower, broccoli, cabbage, mustards, etc.). It also uses moving air to clean the seed. A fan, cool blow dryer, or one’s breath would also be better employed with this technique than trying to use wind.

To use this method:

1. Lay out a sheet or a tarp. Place a large, flat box in the middle. Position the fan nearby, so that it will blow across the box.

2. Pour the seeds and chaff at one end of a cookie sheet, and place the cookie sheet on the box, so the fan will blow across it, with the seeds at the far end away from the fan.

3. Gently lift the far end of the cookie sheet until the seeds begin to roll down. The moving air should be strong enough to continue to make the seeds roll up the cookie sheet a little bit before they begin to roll back down again. It should not be strong enough to make the seeds fly off the cookie sheet.

4. After all the seeds have rolled to the bottom and the chaff has blown away, turn off the fan. If necessary, gather the seeds at one end of the cookie sheet and repeat the process until all the seeds are clean.

3. Screening with Sieves

Using a stack of sieves is one of the simplest methods to clean seeds, though it requires tools that you probably don’t have just lying around. However, the sieves come in handy in a surprising number of ways, so if you decide to save your own seeds, even for one year, I would recommend getting yourself a set of sieves.

To use them is very simple.

1. Stack the sieves so the largest screen is at the top and the smallest screen is at the bottom.

2. Pour the seed matter on the top of the stack, and shake the sieves back and forth for a minute or two.

3. Somewhere in the stack will be a sieve that contains mostly seed and very little chaff. Where the seeds end up will depend on their size.

4. If you need to clean the seeds a bit more, gently blow across them to remove the bits of chaff that ended up on the same sieve tray.

4. Electrostatic Separation

Electrostatic separation is something I was doing – before I knew there was a term for it. I was trying to clean some seed (I think it was lettuce seed) and having no luck whatsoever. The seeds were just too light and I was losing as much seed as I was chaff.

I got frustrated, poured the whole lot in one of my plastic kitchen cups, and set it on the table. It stayed there for 2 or 3 days. When I finally came back to it, I noticed that some of the chaff was stuck to the side of the cup. I suppose the slight movement between the cup and the tablecloth had produced the static charge.

I dumped the seeds into another cup, and tried to make it happen again. It worked.

I took the cups into the living room and, using the stronger charge of the carpet, I poured a tablespoon or two of seeds into one cup, and then rubbed the bottom of the cup on the living room carpet, swirling the seeds around the cup as I did. More chaff stuck to the sides, and the seed was left clean.

I repeated this several times until I’d cleaned the whole batch of seed.

Why did the chaff stick to the sides of the cup and not the seeds? I can only presume it was because the seeds still had more moisture in them than the chaff did. I did have a small handful of seeds that stuck to the sides of the cup, but not many. Likely they were the smaller, non-viable seeds.

To be honest, at the time, I was wondering if creating the electrostatic charge would negatively affect the seeds (making them less likely to germinate or something), but they were just fine. And then I found out later that some people have used this method for quite a long time.

Funny how things happen, sometimes.


4 Responses to Cleaning Your Seeds: Separation & Winnowing Methods

  1. durotimi roland July 18, 2017 at 10:03 am #

    educating,enlighten,and intellectual eye opening

  2. ML September 9, 2017 at 7:09 am #

    Ha! You said ‘… electrostatic charge would negatively affect the seeds.”
    Nice pun.

    • Anni September 23, 2017 at 8:52 pm #

      I didn’t catch that before. 🙂

  3. Doug November 19, 2017 at 2:17 pm #

    Thanks, well written, you are quite knowledgeable. Thanks, Doug


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