Clean Seeds, Happy Plants: The Importance of Seed Cleaning

When cultivating a garden, a great pleasure arises when allowing the plants to mature and produce seeds, which can then be collected and stored for future planting.

Harvesting the seeds is a crucial part of this process and the health, longevity, and germination success of those seeds depend on how you harvest, clean, and store them. 

After you collect the seeds, you need to dry and process them before you can safely store them. There are many ways you can thresh and winnow the dry seeds. Read more to find out how to clean and process your seeds.


The first step in collecting your seeds is to wait for them to ripen on the plant. Whether the seeds develop in pods, exploding seed heads, or capsules, you should give them enough time to reach maturity on the plant before you can harvest them. Signs of maturity vary depending on the specific plant. 

But in most cases, the seed heads will change color from green to yellow, brown, red, or black as they dry up and become easier to pluck. The best time to collect the ripe seed heads is on a dry day around noon. 

In the case of fruit and berry seeds, you can collect the seeds by crushing the fleshy fruits or berries in a sieve, removing the pulp, and rinsing the seeds at the bottom of the seeds in cold water. 

For nuts, you should wait for them to ripen and start to fall to the ground. Place a sheet on the ground under the tree and shake the branches. The ripe nuts will drop on the sheets. Collect them and put them out to dry.


Even if the seed heads look dry, the seeds inside still have moisture. Lay the seed heads on a clean sheet in a cool and dry place in your house. Make sure the area is well-ventilated and give the seed heads time to dry out. An airing cupboard or a bench in a greenhouse are both ideal for this process.

Some seed heads need extra attention while drying. Exploding seed heads as is the case with Euphorbia lathyris plants tend to snap out and spread the seeds everywhere once the seed heads are dry.

Fruit and berry seeds need to be placed on a paper towel to dry. It might take anything from a few days to a couple of weeks for the seeds to dry out completely.

Threshing – 3 Methods

Once the seed heads are dry, it’s time to extract the seeds and get them cleaned up. How you extract the ripe seeds depends on the plant species and what type of seed head they come in. Some seeds have feathery bits attached to them while others come in hard pods that need to be crushed. 

Even other types of seeds such as exploding seed heads, catkins, and winged seeds, they all have extra parts of the plants that need to be removed from the seeds. You can use their hands, feet, or specific equipment for threshing. It depends on the type and amount of seeds you’re threshing. That said, the main methods of threshing seeds are beating, crushing, and shaking. 

Method 1. Threshing/Beating

Some seeds need to be extracted by crushing the seed heads. This applies mostly to the seeds that come in pods and capsules such as beans. Place the dry seed heads in a bucket or pile them on a clean sheet on the ground. Wear shoes with rubber soles so as not to damage the seeds while crushing the seed heads.

Step inside of the bucket or walk over to the pile on the sheet and start trampling them with your feet. Don’t stomp too hard, otherwise, the seeds might break or start flying all over the place.

Once all the seed heads are crushed, you can manually extract the seeds from the chaff. Remove any parts of the seed heads still attached to the seeds then prepare them to be winnowed.

Method 2. Rubbing/Crushing

Not all seeds can be trampled on with your feet. Some seeds are delicate and would break under pressure. These seeds should be rubbed by hand to break the seed heads and extract the seeds inside. You’ll need to wear gloves to protect your hands against shards and splinters.

Place the pile of seed heads in the bucket and work your way through them. Grab a handful of seed heads in your palm and place the other palm on it and apply gentle pressure while rubbing your hands together. This should be enough to crush the outer shells and free the seeds inside.

Another way to crush the seed heads without having to step on them is to place them on a hard surface and apply pressure with your hands in a rubbing motion. Test this on a small sample of the seed heads first to make sure you’re not damaging the seeds with forceful rubbing.

Method 3. Shaking

Seeds that come in exploding seed heads don’t need much to extract them. All you have to do is place the dry seed heads in a bag and give them vigorous shaking. The friction will cause the seed heads to snap open and free the seeds.

Go through the debris to make sure you have all the seeds free. If some seed heads are not cracked, place them between your thumb and forefinger and press firmly. They will crack open giving you access to the seeds inside.

Winnowing – 3 Methods

After threshing the seed heads, you’re usually left with a handful of seeds inside of a pile of chaff. The next step is to sort this out to separate the seeds from the chaff. This is called winnowing. You use the wind to blow away the lighter materials (the chaff) and leave the heavier materials (the seeds) behind.

Grains are the type of plants that need winnowing. Whenever you have seeds that are heavier than the chaff, then winnowing is the right process to extract the seeds. Winnowing is cost-effective since it doesn’t require special equipment. In general, you can winnow a pile of crushed seed heads using moving air, sieves, or static electricity.

Method 1. Moving Air

One way to winnow your grains from the husk or chaff is to expose them to moving air. You will need to do this outdoors where you can drop the mixture of seeds and chaff from a height such as a roof. Place a sheet on the ground below you to collect the seeds. The wind will blow away the husk before it reaches the ground.

Another way to use moving air to winnow the seeds is to place the mixture on a sheet out in the open. Switch a desktop fan next to you and set it a couple of feet from the pile. Stir the mixture by throwing it in the air with your hands. The wind from the fan will blow away the chaff while the seeds fall back on the sheet. Continue to do that until all the chaff is gone.

Method 2. Sieves With Various Mesh Sizes

Winnowing can also be done using sieves. Even the grains that need moving air to winnow still have to go through sieves to separate the seeds from dirt and debris. Choose a sieve with the right mesh size that is smaller than the size of the seeds you want to winnow. 

Spread the seeds over the mesh of the sieve and give it a few shakes to let the debris and dirt drop. You might also have to rub the seeds into the mesh to crush the debris and force it out. Pick any chaff, dirt, or debris left with your hand or with a pair of tweezers and throw it out.

Method 3. Static Electricity

Some seeds such as torenia seeds and artillery plant seeds are too tiny to use moving air or sieves to winnow them. The only thing that works, in this case, is using static electricity. Place the mixture in a ceramic bowl and swirl it around a few times.

Empty the content in another ceramic bowl. You’ll notice that the tiny particles such as dirt and plant debris are clinging to the sides of the first bowl while the seeds remain at the bottom.

Clean the first bowl and swirl the mixture in the second ceramic bowl. Then empty it into the first bowl. Repeat until you have nothing but seeds left in the bowl.

Storing Seeds Properly

Once you have the seeds cleaned, crushed, and winnowed, you’re ready to store them. Here are a few tips on how to store seeds properly.

  • Make sure the seeds are perfectly dry.
  • Keep the seeds in airtight containers such as glass jars with gasketed lids.
  • Wrap two tablespoons of powdered milk into four layers of facial tissue and stash them with the seeds in the container to keep them dry.
  • Label each jar or container with the name of the seeds and the date you stored them.
  • Keep the seeds in a cool and dry place. 


Harvesting the seeds is only half the process. You need to clean, crush and winnow the seeds the right way to ensure their health, vigor, and longevity.