After a week or two of watching your microgreens flourish, the exciting moment arrives: harvest time! Harvesting microgreens is quick and easy, but doing it the right way will ensure you get the best flavor, maximum nutrients, and a good shelf life from your greens. In this guide, we'll cover when to harvest for peak flavor, the proper harvesting technique to avoid waste or contamination, and how to store your microgreens so they stay fresh (and don't turn to slime in the fridge). With these tips, you can enjoy the fruits - or rather, the shoots - of your labor at their very best.
When to Harvest Microgreens for Peak Flavor and Nutrition
Microgreens are typically harvested quite young - that's the whole point (they're "micro"). The general rule is to cut them once they've developed their first set of true leaves. Let's break down what that means:
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When seeds germinate, the first leaves to appear are the cotyledons (seed leaves). They often look like a pair of small leaves and are actually part of the seed embryo. After those, the plant starts growing its true leaves, which are the leaves that resemble the mature plant's foliage.
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For many varieties, you'll see the true leaves coming in a few days after the cotyledons open. For example, broccoli microgreens will show tiny frilly true leaves around 8-10 days after sowing, right after the smooth oval cotyledons. Pea shoots have small leaflets and tendrils as true leaves around day 10-14.
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Ideal harvest time: Usually 7-14 days after germination, depending on the crop. Many fast growers (radish, broccoli, mustard) are ready in about 7-10 days. Others like sunflower and pea might take 10-14 days to get good size. Some herbs (basil, cilantro) take longer, ~16-20 days. But since we're focusing on beginners' microgreens, most of your crops will be in that ~1 to 2 week range.
A key indicator is the height and leaf stage:
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Height: Most microgreens are harvested when about 3-8 cm tall (1-3 inches), depending on variety. For instance, radish might be 5-8 cm tall with robust stems at harvest, whereas basil microgreens might be only 3-4 cm tall but have a couple true leaves.
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Leaf stage: As mentioned, at least one set of true leaves. Some, like radish and cabbage microgreens, taste great even at the cotyledon stage (in fact radish is often harvested then to avoid a spicier true leaf). Others, like rocket, you want that first true leaf for the real peppery punch. Pea shoots you typically let grow a bit taller (maybe second set of true leaves or tendrils) to get more stem length.
If you're unsure, sample a few! Snip a couple and taste them. The flavor can change as they grow:
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Too early (only cotyledons): sometimes a milder or not fully developed flavor. But for mild brassicas (like broccoli) that's fine. For radish, cotyledon-stage is actually strong and good. For peas, you wouldn't harvest at just cotyledon because that's basically a tiny nub.
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Ideal stage: good size and vibrant taste - e.g., sunflower shoots are sweetest just as their cotyledons fully spread and maybe a tiny bud of a true leaf shows; any later and they can get fibrous.
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Too late: Microgreens left too long (taller than ~10-15 cm or with multiple true leaves) often start to get fibrous or bitter. For example, arugula microgreens become intensely bitter if you let them go to 3-4 true leaves. If radish microgreens grow their true leaves and even hint at a second set, they often develop a bitter, somewhat unpleasant flavor. Also, older microgreens may get woody stems (especially pea and sunflower if left too long) and they might have depleted the nutrients in their medium, becoming yellowish.
Another reason not to wait too long: risk of spoilage. The longer you keep microgreens unharvested past their prime, the more likely you'll see mold or damping off or just decay as they outgrow the tray's capacity. Remember, microgreens are usually harvested well before they'd need any additional fertilization - they're living off seed energy and maybe some soil nutrients. Past that, they get weaker or need feeding.
So in summary: harvest promptly when they're ready. Most beginners are eager anyway, but don't hesitate thinking "maybe they'll get bigger leaves if I wait." They will, but at cost of quality. It's better to sow successive batches than to let one batch grow too long.
(If you want baby greens or a secondary harvest - note that most microgreens will not regrow after cutting, unlike say cut-and-come-again lettuce. You sow anew each time. Pea shoots are one exception - they can sometimes regrow for a second, smaller cut. But typically, plan one harvest per sowing.)
Harvesting Technique: How to Cut Your Microgreens
Harvesting microgreens is straightforward, but a few pointers will ensure you get clean, sand-free, long-lasting greens:
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Tools: Use a sharp pair of scissors or garden shears, or a sharp knife/blade. Many growers like scissors for ease. If using a knife, a very sharp kitchen knife can slice through a bunch in one go. The key is sharpness - you want to cut, not crush. A clean cut minimizes damage to the plant and keeps edges from browning.
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Sanitize tools: Since microgreens are eaten raw, you want to avoid introducing bacteria. Wipe your scissors or knife with rubbing alcohol or a mild bleach solution (then rinse) before starting, especially if you've used them for other gardening tasks. Also wash your hands or wear disposable food-safe gloves if being extra cautious (important if you plan to store them or serve to others). Commercial growers often wear gloves to prevent any contamination.
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Harvest dry: It's best to harvest when the plants are dry - not right after watering. If you water in the morning, let them dry a few hours or harvest the next day. Wet microgreens cut and stored tend to decay faster. In fact, one tip is to stop watering 6-12 hours before harvest if practical, to let plants transpire and be crisp (not too limp though from lack of water, just not wet). If you run a fan, you could use it to gently dry the leaves before cutting. This reduces the surface moisture and prolongs shelf life.
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Cut above the soil: When harvesting, hold a bundle of microgreens upright (or you can just let them stand and use your tool) and cut just above the soil or growing medium line. Essentially, you want to avoid getting any seed hulls, roots, or soil in the mix. Cutting too low can grab bits of the medium (especially soil) - biting into gritty microgreens is no fun and it will also introduce decay organisms. Cutting too high wastes part of the edible stem. Aim to slice all stems about 1-2 mm above the medium's surface. With a good tray, they should have grown pretty uniformly, so you can often shear straight across like giving them a flat-top haircut.
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Cut in batches: You don't have to cut the entire tray at once if you only need a little. Microgreens can stay alive in their tray a bit longer. In fact, if you plan to use them over 2-3 days, some prefer to leave them unharvested and cut right before use for maximum freshness. However, note that once they're at prime stage, they might start declining if left too long. If it's only a day or two, leaving some in the tray is fine (just keep watering lightly). For a longer period, it's better to harvest and refrigerate (as the tray environment might lead to rot). Many home growers will just harvest as needed for a meal.
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Work quickly in a cool environment: If your home is warm, try harvesting in the cooler part of day (morning or evening). Heat can wilt microgreens fast after cutting. Ideally, harvest, then get them cooled soon (more on that in storage). Commercial operations often harvest in a cool room or bring trays into a cooler space for cutting, then move produce straight into refrigeration. As a home grower, just avoid leaving cut greens sitting out at room temp for too long.
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Cleaning the harvest: If you've done it right, your harvested microgreens shouldn't need washing - they should be pretty clean (grown indoors in a clean medium). In fact, not washing is often recommended because any added water can reduce shelf life. Microgreens are fragile; washing and handling can bruise them, and moisture encourages rot. However, if you do see some soil bits or you just prefer to wash (or if you used any foliar feed or something), do this gently:
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Fill a bowl with very cold water, gently dunk the harvested microgreens and swish lightly.
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Quickly remove and spread on paper towels or a salad spinner lined with a tea towel, and dry them thoroughly. A salad spinner on low can help, or pat and air-dry on towels. They must be dry before storing.
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Only wash if necessary, and ideally right before use, not before storage (unless you can dry them perfectly). There is research that washing can damage them and create entry points for bacteria, so many choose not to.
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(If you've grown in soil and got a bit of dirt on lower stems, a wash might be needed. Hydroponically grown microgreens usually don't need any washing because there's no soil.)
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Avoid cutting too far ahead: Microgreens taste best fresh-cut. If you cut them and leave out, they'll start wilting within an hour or two (especially radish, sunflower - they flop fairly quickly once cut at room temp). So plan to cut, then either use immediately or get them into the fridge soon.
A note on yield: Don't be surprised that once cut, microgreens collapse into a much smaller mass than how they looked growing. A full 10x20 inch tray might give only 100-200 grams of microgreens depending on variety. That's normal - they're 90% water. Handle that precious pile carefully.
Now, what about after harvest? We recommend promptly getting your harvested microgreens into storage if not eating right away.
Storing Microgreens to Extend Shelf Life
Fresh is always best - if you can eat your microgreens right after harvest, you'll get maximum crunch and nutrition. But you can store them for later use, typically about 5 to 7 days in the refrigerator with proper methods. Some tips for storage:
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Cool them quickly: The enemy of produce is field heat. Even in microgreens, after cutting they respire and degrade. So pre-cool if possible. After harvesting, place the greens in a breathable container and pop them in the fridge soon (within half an hour). In commercial terms, we bring them to below 5°C fast. You could even pre-chill a container or the whole tray of microgreens before cutting (some will put trays in a cooler for 30 minutes then cut). But for home, just don't let them sit on the counter.
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Storage container: Use a clean food-grade container. A plastic clamshell, Tupperware, or a resealable bag can work. Line the container with a paper towel or clean cloth. This towel will absorb excess moisture and keep humidity balanced. Microgreens need a bit of humidity to stay crisp, but not direct wetness. The paper towel trick is key - it prevents that slimy buildup. You can place a folded piece at the bottom and even on top of the greens if it's a container.
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Loose cover: You don't want a completely sealed environment because if any moisture is in there, it can't escape and will cause rot. It's often said to store loosely covered. For example, put the lid on but don't snap it airtight, or poke a few holes in a bag. Alternatively, use vented clamshells (like the ones berries or salad mix come in). This maintains high humidity but allows gas exchange. High humidity (near 95-100%) is actually good for microgreens - it keeps them from wilting. Professional storage is at ~98% relative humidity, but excess water on leaves is not good. That's why the towel and slight ventilation help: humidity stays up, condensation stays down.
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Temperature: Store at fridge temperatures, ideally 1-4°C. The colder end (just above freezing) will keep them freshest longest. Do not freeze - if they accidentally freeze (even at 0°C for a bit), they'll turn mushy dark green upon thawing. So make sure your fridge isn't so cold that these tiny greens freeze. Some people store herbs in the crisper, but microgreens are delicate; I'd keep them in the main fridge compartment where temps are stable. Also, avoid the back wall if your fridge sometimes freezes items there.
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Darkness: Keep them in the dark once harvested (fridge is dark with door closed). Light can degrade nutrients like carotenoids, but more importantly can trigger some greens to continue minimal photosynthesis which might cause condensation (not a huge issue, but dark is standard for stored produce).
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Do not store with ethylene-producing fruits: Ethylene is a ripening gas from fruits (apples, bananas, tomatoes, etc.). It can cause leafy greens to yellow and spoil faster. Microgreens are very perishable and can be sensitive to ethylene. So keep them away from fruits in the fridge. If in a container, it's usually fine, just don't put them next to a pile of apples.
If you follow these steps, your microgreens can often last a week. However, some types inherently store better than others. From experience:
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Pea shoots and sunflower shoots store quite well, often 7-10 days if dry and cool, as they're a bit sturdier.
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Radish, mustard, cabbage microgreens store moderately (5-7 days) but can start to yellow or get root-hair slime if not dry.
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Broccoli microgreens tend to stink if they go bad (they have sulfur compounds) so use those within 5 days ideally.
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Basils and other herbs - actually, basil microgreens hate the cold (basil darkens below 8°C). If you grew basil microgreens, they actually prefer around 10°C, but you likely aren't storing those long anyway because of flavor.
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Cilantro microgreens store decently if dry, but like basil they're an herb so best fresh.
Check on stored micros daily. If you see the paper towel is damp, replace it. If any leaves look slimy or off, remove them to avoid spreading rot.
Pro tip: If you need microgreens to last toward the longer end (say a week), harvest a little earlier (just at first true leaf) and store very cold. They'll sometimes even continue slow growth in the fridge (you might see true leaves get a bit bigger). The nutrient content can remain high - studies show microgreens hold nutrients fairly well under refrigeration for a few days, though some vitamins like vitamin C will diminish over time.
When you're ready to use stored microgreens, take out only what you need and return the rest quickly to the fridge. Rinse them right before use (if you feel the need to rinse; if they are clean and you didn't previously wash, they should be good to eat straight). Pat dry if you rinsed. Then top your dishes - enjoy that homegrown freshness!
Finally, post-harvest cleanup: After harvesting, compost the leftover soil and root mat (it makes great compost). Clean your trays thoroughly (hot soapy water, maybe a mild bleach if you had any mold issues) so they're ready for the next sowing. Starting with clean trays helps ensure the next batch will grow without problems.
By harvesting at the right time and storing properly, you can make the most of your microgreens. There's nothing like having a jar of pea shoots or spicy radish micros in the fridge ready to toss on any meal. But truth be told, they often taste so good, they might not make it to storage - munching a fresh harvest as a "gardener's snack" is one of the joys of growing microgreens!
Enjoy your harvest, and keep the cycle going by planting the next seeds. Happy microgreen gardening!