How to Harvest & Store Microgreens: The Complete Guide

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Microgreens for Harvest

Microgreens can be easy to grow for many gardeners wanting to be good stewards of the earth, both new and experienced. However, the process for harvesting and storing them can be a little more delicate or complex, depending on the age of the microgreen.

How do you harvest and store microgreens? To harvest standard microgreens (10-14 days old), cut them above the soil line (or above the mat for hydroponic growers). When storing, first wash and then keep the microgreens in a breathable plastic container in the refrigerator until ready for use.

Gardeners can undoubtedly reap the benefits of God’s work in these beautiful, life-giving plants, as long as they are harvested and stored correctly. However, to do that, gardeners first need to understand the different stages of microgreen growth; the right time to harvest will depend on what is wanted out of said microgreens.

About Microgreens

Microgreens are “young, tender, edible crops that are harvested as seedlings,” usually for the purpose of consumption with a variety of delicious cuisines. (Source: University of Kentucky)

Benefits of Microgreens

  • As mentioned before, microgreens take minimal time and effort to grow, but they are also very inexpensive to plant and care for since they only require the basic plant needs.
  • They are small and manageable enough to be grown outdoors or indoors, making them an ideal gardening project for gardeners with limited room in the home or who do not have a lot of time to tend to a full garden.
  • Microgreens are versatile plants.  They are often grown and used in salads or sandwiches or as a garnish in many cuisines, either commercially or for personal dishes. This is due to their strong flavor profiles—they may be small plants, but they offer memorable tastes for any food you pair them with. Some people even use microgreens in nutritional shakes since they provide an abundance of healthy nutrients.

Varieties of Microgreens

A high number of vegetable, herb, and agronomic crops and their several variations can be used for microgreen production. Some popular microgreen crops include:

  • Amaranth
  • Arugula
  • Asian Greens
  • Basil
  • Beet
  • Broccoli
  • Buckwheat
  • Cabbage
  • Carrot
  • Celery
  • Chives
  • Cilantro
  • Collards
  • Cress
  • Dill
  • Fennel
  • Kale
  • Kohlrabi
  • Lemongrass
  • Mizuna
  • Mustard
  • Nasturtium
  • Onion
  • Parsley
  • Popcorn
  • Radish
  • Spinach
  • Sweet Pea
  • Swiss Chard
  • Tatsoi

This is only the beginning of the list! Gardeners can choose many more varieties to grow as microgreens. For a more extensive list, visit the Johnny’s Selected Seeds website.  This will provide information on the seemingly infinite varieties available on the market today.

Microgreen Growth Stages

Microgreens are often also referred to as sprouts or baby greens or plants, but in actuality, these are terms for the different stages a microgreen plant goes through as it grows. Although these different versions of microgreens are similar as they all start as seeds, each stage offers gardeners a unique microgreen experience, as they have different looks and tastes when harvested.

 SproutsMicrogreensBaby Greens
DescriptionSprouts are seeds that have recently germinated or are beginning to grow into a plant. With the nutrients from the seed, it develops a stem, which appears as a shoot growing from the seed.Microgreens are the slightly older version of sprouts that have been planted in soil or a soilless medium. They are usually considered a “microgreen” once they have produced their first set of leaves.Baby greens are essentially microgreens that are typically grown spaced apart from one another. They are leafier compared to microgreens, and are harvested right before they have reached maturation, or become a fully grown plant.
AgeSprouts are quite young—usually around 3-5 days old.Microgreens are typically 10-14 days old; however, slow-growing varieties may be as old as one month.Baby greens are at least 14 days old but can be older—up to 40 days.
GrowthSprouts thrive in a very humid, high-moisture environment, and typically do not require soil or any other type of media to germinate.Microgreens can grow best in soilless media or solely water. At this point in the growing period, microgreens may have their first true leaf features.Baby greens thrive in a soil or soilless mix. At this stage of growth, baby greens have definite true leaves but are technically still considered an immature plant.
HarvestThey are usually harvested to be eaten whole, rather than only its small leaves or tubers alone.Microgreens are typically harvested by clipping the small leaves from the stems, although both parts can be used in cuisine.True leaves and stems are mostly harvested from baby greens for consumption.

(Source: Oregon State University)

How to Harvest Microgreens

When and how microgreens are harvested will depend on in which stage of growth they are collected.



Sprouts can be harvested within a day or two of germination. (Source: Iowa State University)

All of a sprout can be consumed, from its roots to its early growing leaves, so when it comes to harvesting, not necessarily much is needed to remove them from their container.

A key step after sprout removal is to de-hull them. In de-hulling, gardeners remove the seed hulls from the sprout; this is especially important for Brassica sprouts such as cabbage, broccoli, radish, mustard, etc. Since the hulls are large and can hold a lot of water, performing this step will allow the sprouts to have a longer storage life.

To de-hull sprouts after harvest, follow the below steps:

  1. Place the sprouts in a large bowl filled with cold water.
  2. Loosen the sprouts by pulling them apart with fingers or a fork while they are in the water. The hulls will float to the surface.
  3. Skim the hulls off of the surface of the water.
  4. Drain the sprouts, making sure to remove as much excess water as possible. (Note: A salad spinner is a helpful tool to use for this step.)

(Source: Academia)


Kale Microgreens

After a healthy growth period of 10 to 14 days, the microgreens will be ready to harvest. A visual sign that they are ready is when the first true leaves emerge (the second set of leaves that appear), or when they are about 1.5 to 2.5 inches tall. (Source: North Carolina State University)

Gardeners usually harvest both the stems and leaves of microgreens for consumption and use in a variety of dishes, but not the roots.  Since they grow in media, they are not edible like their above-soil counterparts.

When harvesting, keep these tips in mind:

  • The best time to harvest microgreens is usually at night or in the morning. (Source: University of Florida)
  • Use a clean pair of scissors to cut them above the soil line (or above the hydroponic mat if grown via the hydroponic system). Alternatively, to cut the microgreens, use a chef’s knife or mechanized shears; the latter is more common with commercial microgreen gardeners.
  • Compost the soil and/or dispose of the pad. Most microgreens are incapable of regrowth once they have been cut above the roots, so it is recommended to compost the mix for future garden projects.

(Source: Oregon State University)

Baby Greens

Baby Greens

Baby greens are usually ready to harvest between 21-40 days after germination, or when they are about four to six inches tall. The harvesting process is slightly different from how one would harvest sprouts or traditional microgreens, in that there are two ways one can harvest:

  • Multiple Harvest – Use a clean pair of scissors to cut the greens above the soil (about an inch from the surface). After harvesting, the plants will eventually grow new leaves from their base, which can be harvested a second time after three to four weeks. Some baby green varieties allow for a third harvest in the right conditions. After the growing season has ended, use the remaining plant and soil for compost.
  • Leaf or Full Harvest – If baby greens are planted four to six inches apart, the option is available to harvest only the outer leaves or even the entire plant. However, in most cases, the plant will be unable to produce more leaves for additional harvest periods. It is recommended to use the remaining stems and soil for compost.

After harvest, be sure to remove any soil or grit from the plants by rinsing them under cold running water several times.

(Source: University of Maryland)

Honor the Lord with your wealth, with the first fruits from your entire harvest.

Proverbs 3:9

Which Microgreen Growth Stage is Ideal for Harvesting?

The sprout, microgreen, and baby green stages are all suitable times to harvest microgreens. However, when gardeners decide to harvest will depend on what they want from the microgreens.

  • Sprouts are rich in essential nutrients and enzymes and are high in protein. They are also much easier to digest compared to the later microgreen forms. For these reasons, some gardeners may prefer to harvest these microgreens at a very young age.
  • Microgreens have been found to have almost 40 times the nutrition level of their more mature relatives, and a much stronger taste as well. It is because of this that most gardeners choose to harvest their microgreens at this stage.
  • Baby greens are also more nutritious as a microgreen in comparison to their mature counterparts. They are quite tender and offer a different flavor and texture that some food connoisseurs prefer over mature versions.

How to Store Microgreens

Microgreens Storage

Like with harvesting, how microgreens are stored depends on which stage of the growth process they were harvested.


Once the sprouts have been de-hulled and drained of water, store them in the fridge. They keep longer if they are well-drained—especially if they are dry—and in a container that can breathe. Any other type of container, such as a Ziploc bag, will not keep sprouts fresh; before long, they can become quite slimy.

To extend the life of sprouts, be sure to remove and rinse them every few days and drain well before putting them back in storage; this will keep them from drying out quickly. If any of the sprouts are beginning to mold, they should immediately be discarded.

(Source: Academia)


It can be difficult to store microgreens because they do not hold up very well after a short period of time—especially in refrigerated conditions—so, it is often recommended that once they are harvested, they should be rinsed and used immediately. However, there is a way for gardeners to maintain the freshness of microgreens for at least a few days.

(Source: Oregon State University)


Microgreens will need to be washed and then stored in a plastic container in the fridge. Through this method, they can last up to six days. For better storage results, keep the microgreens in a container with air holes. (Source: University of Florida)

Alternatively, lightly wrap any unwashed microgreens in a damp paper towel to store in a Ziploc bag. Ideally, they should be placed in the crisper drawer of the refrigerator. Microgreens can stay fresh this way for roughly five to seven days.

Baby Greens

The ideal way to store baby greens for long-lasting freshness is to store them in the freezer:

  1. After rinsing freshly harvested greens, cut or tear large leaves as desired (smaller leaves can be frozen whole).
  2. Blanch the greens in small quantities, roughly four cups of packed greens per gallon of boiling water. The blanching time starts when the water returns to a boil; the average recommended time for blanching is about two minutes, although it will differ depending on the baby green variety. (Note: This step is important! If the baby greens are not properly blanched, they could lose their flavor quickly while in storage.)
  3. After blanching, cool the greens in a large bowl of ice water for the same amount of time as blanching.
  4. Drain the greens thoroughly until mostly dry and pack in freezer-safe containers.
  5. Cover the container with ice water. There should be about a half-inch space between the container top and the water surface.

Baby greens can be stored in the freezer in this way for eight to 12 months. Be sure to write the date when the greens were placed in storage to keep track of their expiration date.

An alternative way to store baby greens is inside the refrigerator in a breathable container if they will be consumed within a week’s time—although consumers reap the maximum nutritional benefits from them when consumed immediately.

(Source: University of Minnesota)

Preparing for Next Season

Microgreens are unable to regrow after harvest, so after they are harvested, it is recommended to prepare for the next growing season.

When it comes to microgreens, they are fairly simple to grow; all that is needed are seeds, trays—or some other type of container to plant them—and organic soil. Depending on where the microgreens will be growing, an additional light source or method of temperature control, such as a heating mat, may also be necessary. (Source: Oregon State University)


Microgreen Sunflower Seeds

It is recommended that gardeners invest in many seeds for growing microgreens. Enough should be obtained to plant roughly 10 to 12 seeds for every square inch of soil for smaller seeds, or 6 to 8 seeds per square inch if they are larger.

In addition, an important decision is to be made when it comes to choosing which microgreens a gardener wants to grow next season. Technically speaking, almost any herb or green can grow as a microgreen. However, over 80 microgreen-specific varieties are out there for gardeners to also pick from, from milder microgreens to spicier microgreens, and from fast-growing to slow-growing microgreens. (Source: University of Florida)

Milder Microgreens

Mild microgreens are usually plants that are often eaten when they have become mature. Some common mild microgreens include:

  • Chard
  • Amaranth
  • Mizuna
  • Cabbage & Kohlrabi
  • Amaranth
  • Basil
  • Beet
  • Broccoli & Cauliflower
  • Chia
  • Cilantro
  • Clover
  • Tatsoi
  • Sunflower*
  • Peas*

*Note: These microgreens are typically much easier to grow and are a favorite of those new to gardening.

(Source: Oregon State University)

Spicier Microgreens

For those looking for a microgreen that offers just a little more of a stronger taste, try growing one of the following varieties:

  • Mustards
  • Radish
  • Arugula
  • Cress
  • Pak Choi
  • Rutabaga & Turnip

If there is a more specific flavor of microgreen you are trying to find, a good resource is the comparison chart on the Johnny’s Selected Seeds website. On this website, you will find charts for both slow-growing microgreens and fast-growing microgreens. Their full catalog with pictures of the different microgreen types is also available for viewing here.

For those who are ready to purchase more microgreen seeds, different varieties can be found at a local gardening center or online sources, where full microgreen growing kits such as the HAMAMA Home Microgreens Kit (Amazon Link) can also be found.


Microgreen Seed Trays

Microgreens can be grown in any type of container, as long as it has access to moisture, nutrients, air, and light.

Because most microgreens are harvested at a young age, many gardeners choose to use trays (such as the draining saucers of plant containers) to plant them. This is ideal if a few saucers are just lying around in-between growing seasons. Microgreens do not take long to grow, so this is a great temporary option. (Source: Oregon State University)

Gardeners who plan on growing soil-based microgreens need to make sure that the container being used has drainage holes, or is made of a material that can be poked or drilled through to create holes. This ensures that excess water can drain out of the soil without waterlogging and suffocating the delicate microgreen roots.

However, for gardeners who are growing microgreens using the hydroponic system, a container without drainage holes is fine, as this system relies on the seeds constantly having access to water.


Two main ways to grow microgreens exist: the soil-based system or hydroponic system. The growing method that will work best for certain microgreens will depend on their type and variety.

  • Soil-Based System – This system is the traditional planting system in which seeds are planted into the soil and watered regularly. Many larger-seed or sensitive microgreens prefer the soil, such as beets, buckwheat chard, cilantro, peas, and sunflowers.
  • Hydroponic System – This system involves placing the seeds on top of a thoroughly wet mat or piece of wood fiber in which the microgreens’ roots will eventually take hold. The key to a successful hydroponic system is to ensure the seeds always receive water and are placed in a warm area as they thrive in humid conditions.

A few microgreen varieties are out there that can thrive on either a soil-based system or hydroponic system equally, such as:

  • Basic/Spicy Salad Mix
  • Basil
  • Chia
  • Golden Acre Cabbage
  • Kohlrabi
  • Radish
  • Tatsoi

(Source: Oregon State University)

Growing Microgreens

Growing Microgreens

The process for growing microgreens will differ, depending on whether a gardener decides to use the soil-based system or hydroponic system:

Soil-Based Growing

Before planting microgreens in soil, some seeds may benefit from a pre-soak in water to increase the likelihood of quicker germination. Seeds that grow well following pre-soaking include larger seeds such as beets, buckwheat, cilantro, peas, and sunflowers. The amount of time required for soaking will depend on the species.

  1. Prepare containers. For microgreens, depending on the container used, only about one-half to two inches of a soilless mix (containing a variety of organic materials rather than field soil) is needed. Moisten the soil before placing it into the tray. Afterward, use a spray bottle to spray a mist of water on the surface. (Make sure that the soil is damp, but not soggy; overwatering soil-based microgreens can attract fungus and cause harm to the plants.)
  2. Plant seeds. Spread the microgreen seeds across the surface of the soil evenly. (Larger seeds may be near touching one another.) Press them into the soil.
  3. Water seeds. Mist the surface of the seeds. Create a humid-friendly environment by placing the microgreen container inside a dark paper bag or dark area of the home. (Alternatively, mist the inside of a large tray and cover the container with it.) Be sure to mist the seeds (and the lid, if used) every twelve hours to maintain humidity.
  4. Move microgreens from dark to light environment. Leave the microgreen container covered for roughly four to five days. After at least four days, uncover the container and relocate it to a sunny area or under a grow light. The container may need to be continually rotated to allow the seedlings to grow straight up.
  5. Maintain microgreens. Routinely check the soil and add water as needed to keep it moist.
  6. Harvesting. Most microgreens are ready to harvest around ten days after the initial planting.

(Source: Oregon State University)

Hydroponic Growing

  1. Prepare containers. Pour water into the tray or container. Cut a growing pad to fit the bottom of the container, and place it inside. Swish the pad at the bottom around to dampen it, then flip it over to fully saturate the other side.
  2. Plant seeds. Spread the microgreen seeds across the surface of the pad evenly. How many seeds it is ideal to plant will depend on the size of the container.
  3. Water seeds. Mist the surface of the seeds. Create a humidity-friendly environment by placing the microgreen container inside a dark paper bag, or use a dark lid or tray to cover it (be sure to mist the interior of the cover). Continue to mist the seeds and lid every twelve hours; no additional water is needed for the pad inside the container.
  4. Move microgreens from dark to light environment. Leave the containers covered between four to five days. After this period, uncover the container and place them under sunlight or some other growing light source. It is recommended to rotate the trays to prevent seedlings from growing slanted.
  5. Maintain microgreens. Keep an eye on the pad inside the container; if it begins to dry out, add more water. Ideally, you should keep water in the container channels, so the pad is able to absorb water as needed.
  6. Harvesting. Like soil-based microgreens, hydroponic microgreens will be ready to harvest in about ten days.

(Source: Oregon State University)

Growing microgreens is easy and a fun endeavor for many gardeners to take on. They can be harvested and stored at any stage of growth, from sprouts to baby greens—although how they are collected and kept will differ as gardeners move from stage to stage.

Ultimately, as long as gardeners are diligent about caring for God’s handiwork and following the above tips, they can raise healthy (and delicious) microgreens.

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Corey Leichty

Hi, I’m Corey and I love using gardening as a way to provide food for my family, learn life lessons alongside my wife, Andrea, and teach life lessons to my two sons. Do you have gardening questions? Not finding what you are looking for? Please feel free to Ask a Question (Click Here!) and I will get back with you as soon as I can!

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