Common Mistakes When Growing Microgreens (And How to Avoid Them)

May 13, 2025

Pea microgreens growing in the Deep Sprouting Tray Set from On The Grow, showcasing healthy, vibrant growth using a reusable sprouting system.

Microgreens are one of the easiest crops to grow indoors or outdoors, making them an ideal starting point for gardeners of all experience levels. Their quick harvest times, low space requirements, and incredible nutritional value have made microgreens a rising star among home growers, chefs, and market farmers alike.

But even though growing microgreens is relatively straightforward, there are some common mistakes that can trip up beginners (and even seasoned growers). The good news? With a little knowledge and attention to detail, you can avoid these pitfalls and enjoy lush, healthy microgreens consistently.

Let’s take a look at the most common microgreen growing mistakes — and how you can steer clear of them for bigger, better harvests.

*Photo: Pea Microgreens growing in our Deep Sprouting Tray Set without a medium.

Over-watering (Or Under-watering)

Water is essential for growing microgreens, but balance is everything. Over-watering is one of the most common mistakes new growers make. If your growing medium stays too wet, it can create an environment ripe for mold, fungal diseases, and even root rot. On the other hand, under-watering can cause your microgreens to dry out and struggle to germinate or grow properly.

How to Avoid It:
Focus on maintaining consistent moisture, avoiding soaking wet conditions. We recommend misting your seeds 1 to 2 times daily during germination, especially in the critical germination phase. While a fine-mist spray bottle works, investing in a dedicated watering tool, like this one here, is highly beneficial. We've used this type of device for years, ensuring consistent watering and preventing hand cramps common with regular spray bottles. A quality misting device helps control moisture more effectively than pouring water directly.

For mediums like Soil or Coco Coir, gauge moisture levels by visually inspecting or feeling the medium. With hydroponic mats, such as our Reusable Silicone Grow Medium, monitor if the mat appears dry or moist.

How to Tell:

Under-watered: Light-colored medium, dry to touch
Under-watered: Microgreens laying flat
Under-watered: Browning roots that can stick when lifted for bottom watering
Under-watered: Poor or patchy germination
Over-watered: Dark, waterlogged medium with pooling
Over-watered: Poor or patchy germination
Over-watered: Foul smell

Poor Lighting Conditions

Microgreens need good light to grow strong and healthy. Inadequate lighting is a quick way to end up with pale, leggy, weak crops that stretch unnaturally toward the light source and lack nutritional density. By having proper light for our Microgreens, that's part of how we end up with such even and fluffy looking trays come harvest day.

How to Avoid It:
If you’re growing indoors, invest in a LED Grow Lights and position it close to the plants — typically within 8 to 10 inches. Microgreens thrive with 12–16 hours of light per day. If using natural sunlight, choose a bright, south-facing window and rotate your trays to ensure even exposure. Good lighting encourages compact, vibrant growth and boosts both flavor and nutrient content.

Sowing Seeds Too Densely

Broccoli microgreens germinating on a silicone reusable grow mat from On The Grow, showcasing healthy root development and vibrant seed sprouting.

It’s tempting to sow lots of seeds to get a thick, lush harvest. However, overcrowding leads to competition for light, air, and water — and can invite mold and disease.

How to Avoid It:
Sow seeds evenly and lightly across the surface of your grow medium. It’s better to have a thin, uniform layer of microgreens than a packed, suffocated tray. You’ll get stronger, healthier plants that are easier to harvest and clean. And you minimize the risk of finding mold in the middle of your tray, which means you've wasted an entire grow since you cannot eat or sell those greens.

At On The Grow®, we recommend slightly adjusting seeding density depending on the crop — for example, radish and broccoli seeds can be sown closer than larger seeds like peas or sunflowers. If you are unsure of how much seed to use, download our two free PDF guides "Free Microgreen Seeding Guide - PDF" and/or "Free Tray Specific Microgreen Seeding Guide - PDF", we created these guides based on our own experiences.

*Photo: Broccoli Microgreen seeds germinating on our Silicone Reusable Grow Medium.

Inadequate Airflow

Poor air circulation is one of the biggest contributors to mold, mildew, and other fungal problems when growing microgreens indoors. Stagnant, humid air creates a perfect breeding ground for disease.

How to Avoid It:
Set up a small oscillating fan near your growing area to keep air moving, or install 120mm fans on each shelf. Gentle airflow strengthens microgreens, helps evaporate excess moisture, and discourages mold growth. Good air circulation is especially important during the critical post-germination phase when the canopy starts to thicken. Just remember that your fan should not be pointed directly at the microgreens or seedlings. Instead, the airflow is just above the canopy. Pointing a fan directly at the greens can cause uneven growth.

High Humidity

While humidity is important for germination and early growth, too much moisture in the air can cause more harm than good. High humidity levels can create a breeding ground for mold, mildew, and other harmful pathogens, which can quickly affect your microgreens. Excess moisture also encourages leggy, weak growth as plants struggle to breathe properly.

How to Avoid It:

To maintain a healthy environment for your microgreens, keep humidity levels in check. One effective way to do this is by using a dehumidifier. This helps to reduce excess moisture in the air, preventing mold and mildew growth while allowing your plants to grow strong and healthy. If you’re growing in a closed space like a grow tent, a dehumidifier is especially helpful in maintaining an optimal climate.

If you notice that your plants are growing slower, have yellowing leaves, or are showing signs of mold, it may be a sign that humidity levels are too high. A dehumidifier will help balance the moisture levels, ensuring your plants thrive and your environment stays clean.

Harvesting Too Late

Microgreens are best harvested when they have developed their first set of true leaves — usually around 7 to 14 days after sowing, depending on the variety. Waiting too long can cause them to become stringy, fibrous, or bitter in flavor.

How to Avoid It:
Keep a close eye on your trays. Once most of the crop has reached about 1.5 to 3 inches tall and the true leaves appear, it’s time to harvest. Harvesting at the right time ensures the best flavor, tenderness, and nutritional punch. If your unsure of when your tray is ready, you can always pluck a couple and give them a taste test.

Using Poor-Quality Seeds

Rambo Radish and Hong Vit Radish Microgreens with vibrant purple and green stems from On The Grow, showcasing fresh, colorful microgreens.

Not all seeds are created equal, and using seeds not intended for microgreens can lead to poor germination rates, disease, or inconsistent growth. Even if seeds look great on the outside, if they haven’t been tested for the specific requirements of microgreens, they may not perform as expected. Over time, this can lead to frustration and wasted resources, especially when you're trying to grow healthy, vibrant crops.

How to Avoid It:
Always purchase high-quality, untreated seeds from reputable suppliers specifically labeled for microgreens. These seeds are typically tested for purity and germination rates, ensuring they’re free from chemical treatments that could impact food safety. Microgreen seeds are carefully chosen for their ability to grow quickly and provide the best yields, unlike regular garden seeds which may not have the same characteristics.

NEVER USE BIRD SEED. We've seen a YouTube video in the past suggesting birdseed for growing microgreens as a way to cut costs, and that’s a BIG NO-NO. After seeing the video, we reached out to birdseed companies, and they confirmed that birdseed isn’t regulated the same way as seeds meant for human consumption.

On another note, while it's rare, we've had a couple of instances where we received a bad batch of seeds from a reputable supplier. These seeds were prone to issues like low germination rates and poor growth. In those cases, we simply reached out to the company, explained the situation, and they were more than willing to resolve the issue or replace the seeds. This is why it’s always important to work with suppliers who stand behind their products. By sticking to trusted sources and keeping an eye on the quality of your seeds, you'll set yourself up for success in growing healthy microgreens.

Here are a few brands we trust:

True Leaf Market – We've been using them for years.
Johnny’s Selected Seeds – Another great option, though a bit pricier.
Amazon – Convenient, but can be more expensive due to third-party sellers.
Mumm’s Sprouting Seeds – Based in Canada, and they offer great quality.

Neglecting Sanitation

Dirty trays, unwashed tools, and unclean grow spaces are an invitation for mold, pests, and pathogens. Even a single contaminated tray can wipe out an entire crop.

How to Avoid It:
Always sanitize trays, scissors, spray bottles, and grow areas before starting a new batch. A simple solution of food-safe hydrogen peroxide or diluted vinegar can be used to clean surfaces effectively, or you can look into other food safe options for cleaning. Good sanitation practices are especially important for commercial growers or anyone selling microgreens to customers. A clean space is a happy place.

Choosing the Wrong Growing Medium

The growing surface you choose plays a huge role in microgreen success. Some mediums dry out too fast, retain too much water, or are single-use and costly.

How to Avoid It:
Opt for a reliable, high-quality growing medium. At On The Grow®, we love using our Reusable Silicone Grow Medium for hydroponic microgreens. It provides a stable surface that allows plant roots to anchor without the seeds falling through the mesh. Plus, it can be reused multiple times after cleaning and sanitizing, saving us money compared to single-use mediums like soil, coco coir, or other hydroponic mats.

When purchasing mediums like soil or coco coir, always choose a reputable brand. We once bought a coco coir brand that caused constant issues with every grow. We’d develop mold and disease with every tray of microgreens, but once we switched to a different brand of medium, everything grew wonderfully. Clean grows and consistent results start with choosing the right base.

Final Thoughts

Purple Kohlrabi Microgreens with vibrant purple stems and green leaves, grown by On The Grow, with a smiling person in the background.

Growing microgreens is simple, fun, and rewarding — but success hinges on a few critical practices. By avoiding common mistakes like over-watering, poor lighting, overcrowding, and sanitation lapses, you’ll set yourself up for bountiful, vibrant harvests every time.

At On The Grow®, we've spent years refining our indoor microgreen growing methods, and we're passionate about sharing what works. Whether you're growing a few trays for your kitchen or expanding into a microgreens business, avoiding these mistakes will help you grow smarter, faster, and more confidently.

With the right knowledge, a little practice, and a commitment to learning, your microgreens can be lush and consistent— delivering beauty, nutrition, and flavor straight from your home to your plate. And if you haven't already, download our free PDF guide "Free Microgreen Troubleshooting, FAQ & Lingo" for even more tips.