Growing microgreens is usually straightforward, but even experienced growers encounter challenges from time to time. Don't be discouraged - almost every microgreens problem has a solution. This guide covers the most common issues (from mold to leggy growth and yellow leaves) and how to fix them. With a few adjustments, you'll be back on track growing healthy, vibrant microgreens in no time.
Common Microgreens Growing Problems
1. Mold or "Fuzzy" Growth: If you notice white, fluffy patches on the soil or stems with a musty smell, you might be dealing with mold. It's important to distinguish true mold from harmless root hairs that many microgreens (like radish or broccoli) produce. Root hairs look like uniform white fuzz along the roots and disappear when misted with water. Mold, on the other hand, appears in irregular patches (often greyish or web-like) on the soil surface and will spread if not addressed. Why it happens: Excess moisture and poor airflow are the main culprits. Overwatering (especially from above), high humidity, warm temperatures, and overcrowded seedlings create a mold-friendly environment. How to fix: Focus on prevention and prompt action. Ensure good air circulation - use a small fan or at least uncover your trays as soon as seeds have germinated to avoid stagnant humid air. Water properly by using bottom-watering once sprouts appear, so the surface stays drier. Keep the room temperature moderate (around 18-24 °C) since heat and humidity encourage fungus. Always start with clean equipment and fresh, sterile growing medium to avoid introducing spores. If you do see a small mold patch, remove that section of the crop and improve airflow immediately to stop the spread. Some growers lightly mist affected areas with a dilute hydrogen peroxide solution to kill surface mold. For a deep dive on this topic, see our guide "What to Do When Microgreens Grow Moldy" (which covers mold vs. root hairs and anti-fungal strategies in detail) - internal link to mold article.
2. Leggy or Floppy Microgreens: "Leggy" microgreens have abnormally long, thin stems. They may grow so tall and weak that they tip over instead of standing upright. Often they'll look pale or yellowish due to lack of chlorophyll. Why it happens: Insufficient light is the #1 cause of leggy microgreens. If sprouts don't get enough light right after germination, they stretch out desperately "looking" for it. This can happen if you keep them in the dark (blackout period) for too long or if your light source is too weak or too far away. High temperatures can also contribute - warmth makes them grow fast and spindly. Overcrowding is another factor, as densely sown seedlings may compete and stretch upward for light and space. How to fix: Give itsy-bitsy greens ample light as soon as they sprout. Once most seeds have germinated, remove any blackout cover and put the tray under a strong light source. A sunny windowsill (south-facing in the northern hemisphere) or a good LED grow light works well. Make sure the light is close enough - even a bright window several feet away can cause stretching, so move trays right up to the window glass (watch out for cold drafts or intense heat). Provide at least 12-16 hours of light daily for most varieties. If you see seedlings leaning towards the light, that's a hint they want more - you can rotate trays daily for even exposure. Keep the room temperature on the cool side (around 18 °C) rather than very warm, to encourage sturdier growth. Finally, avoid overextending the blackout period - most microgreen seeds only need 2-4 days of darkness to germinate. Uncovering them promptly prevents excessive stretching in darkness. Unfortunately, once microgreens have gone leggy and floppy, they won't thicken up again. You can still harvest and eat them, but use this experience to adjust your next crop (more light, shorter blackout, maybe a bit more space between seeds). For more tips on fixing weak, leggy microgreens (and preventing it in the future), see "How to Fix Leggy Microgreens" - internal link to leggy article.
3. Yellowing Leaves: It's alarming to find your microgreens looking pale yellow instead of vibrant green. Not all yellowing is bad - new sprouts are yellow when they first emerge from darkness (before they see light). But if your microgreens stay yellow or start yellowing after they should be green, it signals an issue. Why it happens: The most common cause is, again, lack of light. Plants need light to produce chlorophyll (the green pigment), so if they aren't getting enough intensity or hours of light, they remain yellow. Another cause can be prolonged growth without nutrients - however, in a typical 7-14 day microgreen cycle, the seed's internal food supply is usually enough. Only if you try to grow them significantly longer (3+ weeks) might they exhaust their nutrients and turn pale. Overwatering or fungal issues can also cause yellow, wilting patches - for example, damping off (a soil fungus) can rot stems and lead to wilting/yellowing even if light is adequate. Underwatering, conversely, can make plants droop and pale as they dry out. How to fix: First, give them light! If you realize you kept the tray covered too long or in insufficient light, move it to a bright spot or under grow lights immediately. Most yellowed microgreens will green up within a day or two of proper light exposure. Increase your daily light hours or use a stronger light if needed. Ensure you're not keeping the blackout dome on for excessive days. Next, check watering: Are the plants thirsty? If the growing medium feels dry, water gently (bottom water or light mist) and they should perk up. If instead the medium is waterlogged and you see slimy stems, you might have rot - improve air circulation and let the tray drain; you may need to discard severely affected sections. Note that the seed leaves (cotyledons) of microgreens sometimes turn yellow and drop off naturally once the first true leaves form - that's normal and not a problem. To boost greening in slightly nutrient-deficient cases (e.g. microgreens grown on plain coco coir for longer than 2 weeks), you can try a half-strength organic liquid fertilizer once true leaves appear. However, this is rarely necessary for typical microgreens. Focus on light and proper watering. For a detailed exploration of yellow microgreens and how to restore their color, read "Why Are My Microgreens Yellow? Causes & Cures." - internal link to yellow article.
4. Uneven Growth in the Tray: Sometimes one side of your microgreens tray flourishes while the other side struggles. You might see one corner with tall, ready-to-harvest greens and another corner with short or sparse growth. Why it happens: The two biggest reasons are uneven light and uneven moisture. If one side of the tray gets more light (for example, it's closer to a window or bulb), that side will grow faster. The shaded side will lag behind. Similarly, if your watering isn't uniform, parts of the tray can dry out more quickly (often edges dry out first) or conversely stay too wet, causing slower growth in those areas. Tray levelness matters too - an off-level surface can lead to water pooling in one area and not reaching another. Another factor is seed distribution. If seeds were spread unevenly, some patches might simply have fewer plants. Or if the weight/cover during germination wasn't even, seeds in some spots may not have made firm contact with the soil and thus germinated poorly. How to fix: Ensure even lighting by rotating your tray daily if using sunlight, or use a grow light that covers the whole tray uniformly. Check that your grow space isn't giving one side a different temperature or airflow (avoid putting one end of a tray near a heater or drafty window). Water evenly - it helps to bottom-water by filling the tray underneath, which naturally spreads moisture. If top-watering, mist across the entire tray uniformly. Remember edges often dry out faster, so you may need to rotate or slightly adjust watering to compensate. Using your finger to feel the moisture in the center and corners can tell you if some sections are too dry or too wet. Always drain excess water; a waterlogged center can stunt those plants. For future crops, sow seeds as evenly as possible. Take your time broadcasting seeds so that all areas receive a similar density. Also, use a flat, level surface for your trays. If one side of the tray was lower, that side might have stayed wetter - adjust by leveling or by drilling drainage holes if needed to prevent pooling. If despite best efforts one half of a tray is ready before the other, you can go ahead and harvest the taller side first. Give the smaller side a bit more time and care - it may catch up. Our dedicated article "Uneven Microgreens Growth? Here's How to Fix It" offers more insights on diagnosing and preventing patchy growth - internal link to uneven growth article.
5. Low Yields or Slow Growth: You've followed the instructions, yet your harvest seems skimpy or the microgreens are growing at a snail's pace. If you're not getting the bounty you expected, several factors could be at play. Why it happens: One common reason is insufficient seed - if you sowed too thinly, you simply won't get a full tray of microgreens (commercial growers use specific seed densities for each crop to ensure a lush tray). On the flip side, using old or poor-quality seeds can result in low germination, meaning many seeds never sprout and yield is low. Temperature strongly affects growth speed: microgreens grow fastest around room temperature (~20 °C). In a chilly room (say 15 °C), expect slower germination and growth. Extremely warm conditions (above ~27 °C) can cause issues like damping off or lanky growth that might reduce overall harvest. Water and medium: If the seeds dried out at any point, many will stay dormant or die, giving a patchy, low-yield tray. Conversely, waterlogged conditions can rot seeds or roots, also cutting yields. Light: After germination, insufficient light can slow down growth and result in smaller, weaker plants (they may also be pale or leggy as discussed). Additionally, different microgreen varieties have different yield potential and timelines. Fast growers like radish or mustard might be ready in 7-10 days, whereas herbs like basil or slower seeds like beets and chard can take longer (14-21 days). If you harvest a slow-growing variety at the same time you would a fast one, you'll obviously get less output simply because it wasn't mature. How to fix: First, ensure you are using fresh, high-germination-rate seeds from a reputable supplier - this alone avoids many yield problems. Check seed pack labels for germination rates (anything much below 90% will give noticeably lower yields, and under 75% is problematic). Next, sow enough seeds for the tray size and crop type. Microgreen guides often recommend a certain grams of seed per tray - use those guidelines for a dense but not overcrowded sowing. If you suspect you under-seeded, increase the amount next time. Optimize your environment: keep the growing temperature around 18-22 °C for most varieties, and maintain good humidity (not too dry or too wet). Water consistently - the growing medium should stay moist (but not waterlogged) throughout the grow. If you find growth is slow, evaluate the light: provide plenty of light once sprouts are out of blackout, as this drives photosynthesis and growth. Aim for at least 12 hours of light daily, and consider supplemental lighting if indoor ambient light is weak. Also, be patient and adjust expectations to the crop - for instance, if you're growing cilantro microgreens, they naturally take longer to germinate (sometimes 7-10 days just to sprout) and won't yield as much biomass as something like peas or sunflowers in the same time. Make sure you harvest at the right stage: most microgreens are best cut when they have fully expanded cotyledons and maybe the first hint of true leaves. If you cut too early, yields will be smaller; too late, and you risk spoilage or tough texture. Finally, remember that practice makes perfect. Keep notes on your growing cycles - if a batch had low yield, note the seed amount, variety, and conditions to see what you can improve next time. For a thorough guide on boosting your microgreen harvests and troubleshooting slow growth, check out "How to Troubleshoot Low Yields or Slow Growth" - internal link to low yield article.
6. Other Issues: While the above five are the most common problems, you might face a few other hiccups:
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Poor Germination: If very few seeds sprout at all, consider seed quality and storage. Old seeds or improper storage (too humid or hot) can kill viability. Also, some large seeds need a pre-soak (peas, sunflower, beets) to germinate uniformly. Ensure you keep seeds consistently moist during the first 3-5 days; a mistake many beginners make is letting the seeds dry out after a day or two, which can halt germination. Using a humidity dome or cover for the initial phase helps, but be sure to remove it once most seeds sprout to avoid mold.
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Damping Off (Seedling Rot): This is a specific fungal disease where seedlings suddenly topple over at the base and die. It's often confused with mold. Damping off is usually caused by pathogen-loaded soil, overly wet conditions, and poor air circulation. Unfortunately, if it occurs, affected seedlings can't be saved. The best approach is prevention: use clean, sterile soil and trays, don't overwater, and give seedlings airflow (even a gentle breeze from a fan). If you experience damping off, discard the whole batch (don't eat those) and start fresh with sterilized equipment.
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Pests: Indoors, pests are less common, but occasionally fungus gnats or aphids might find your microgreens. Signs include tiny flies around soil (gnats) or sticky residue on leaves from aphids/whiteflies. Prevent pests by using fresh potting mix (not garden soil that might contain eggs) and keeping your growing area clean. If you do see pests, you may need to dispose of that tray to prevent spreading, or use gentle organic remedies (like neem oil or insecticidal soap) if the crop time allows.
Keep Calm and Keep Growing
Don't be too hard on yourself if your microgreens encounter one of these issues. Even professional growers see mold spots or leggy seedlings now and then - it's part of the learning process. The good news is microgreens grow so quickly that you can troubleshoot and try again almost immediately. By observing your trays daily, you can catch problems early and make small tweaks to your watering, light, or airflow to correct course. Remember, each variety may have its own quirks: for example, sunflower microgreens are prone to a bit of mold due to their thick shells (just give them extra airflow), and pea shoots drink a lot of water so they can dry out faster on the edges. As you gain experience, you'll get a feel for these nuances.
Above all, start with quality seeds and a clean setup. Many problems (poor germination, disease) can be avoided by using fresh, tested seeds with high germination rates and no pathogens. At Deliseeds, we take pride in providing clean, high-quality microgreen seeds so that your growing journey starts off strong. By combining good seeds with the right techniques - proper watering, ample light, airflow, and care - you'll be rewarded with tray after tray of nutritious microgreens. Happy growing, and enjoy the process of learning with each crop! Ready to try again? Browse our Deliseeds microgreens selection for reliable seeds that will set you up for success.