Short answer: prevent microgreens pests and mold with clean trays, fresh seed, the right seed rate, bottom watering and a small fan. For fungus gnats, let the surface dry slightly and use sticky traps. For aphids, rinse them off or remove affected greens. If real mold appears, compost the tray and adjust your setup for the next one.
Common microgreens pests and problems
| Problem | What it looks like | Main cause | Fix |
|---|---|---|---|
| Fungus gnats | Tiny black flies around the soil | Damp soil | Water from below, let surface dry, sticky traps |
| Aphids | Small green or black bugs on leaves | Brought in from houseplants or outdoors | Rinse off, remove affected greens, isolate tray |
| Mold | Gray or colored fuzz, musty smell | Too dense, too wet, still air | Compost tray, sow thinner, add airflow |
| Damping off | Stems collapse at the soil line | Cold, wet soil, poor airflow | Water less, warmer room, clean trays |
| Root hairs (not a problem) | Fine white fuzz on roots, day 2–3 | Normal growth | Mist: they collapse |
Fungus gnats
Fungus gnats are the most common of all microgreens pests. The adults are harmless but annoying. Their larvae live in damp soil.
- Water from below and tip out extra water.
- Let the soil surface dry slightly between waterings.
- Use yellow sticky traps near the trays.
- Use a fresh bag of potting mix, stored closed.
- Try soil-free mats, which gnats like less.
Aphids
Aphids rarely find microgreens indoors but can hop over from houseplants. Rinse the greens gently, or cut and remove the affected section. Keep microgreen trays away from infested plants.
Mold
Mold is the biggest microgreens problem. It's caused by too much seed, too much water and still air. If you see true mold, compost the tray. Then:
- Sow a little thinner. Check the seeding chart.
- Water from below, never over the leaves.
- Run a small fan on low.
- Keep the room at 65 to 75°F (18 to 24°C).
Root hairs vs mold: fine white fuzz on day 2 or 3 is usually root hairs, especially on radish and broccoli. Mist it. Root hairs collapse; mold doesn't.
Damping off
Damping off rots stems right at the soil, and seedlings fall over in patches. It's caused by fungi that like cold, wet, stuffy conditions. Water less, increase airflow, and wash trays in hot, soapy water between crops.
How to prevent microgreens pests: checklist
- Clean trays and tools before every crop
- Fresh seed sold for microgreens
- The right seed rate, not too thick
- Bottom watering after blackout
- A small fan for airflow
- A warm room, 65 to 75°F
- Bright light after uncovering
Natural and food-safe steps only
You eat microgreens within days of sowing, so avoid chemical sprays. Most aren't labelled for microgreens. Prevention, clean equipment and good growing conditions are the safest pest control. If a tray goes wrong, compost it and start fresh. It only costs a little seed.
For more help, see microgreen mistakes and the step-by-step microgreens guide.
Frequently asked questions
What are the tiny flies around my microgreens?
Usually fungus gnats. They breed in damp soil. Let the surface dry a little between waterings, water from below, and use yellow sticky traps to catch adults.
Is it safe to eat microgreens with a little mold?
No. If you see real mold, gray or colored fuzz in patches that smells musty, compost the tray. Don't try to cut around it.
What is damping off in microgreens?
Damping off is a fungal problem that rots seedling stems at the soil line, so they collapse. It's caused by cold, wet soil and still air. Water less, add airflow and use clean trays.
Can I spray pesticides on microgreens?
It's best not to. You eat microgreens within days, and most sprays aren't labelled for them. Focus on prevention and simple, food-safe steps.
Written by Michael
A passionate sprouting professional sharing practical tips for growing sprouts and microgreens at home. More about Michael
