You sowed the tray, covered it, waited — and nothing happened, or only a patchy scattering of seeds came up. Germination problems are frustrating, but they are almost always caused by one of a handful of things: the seed, the temperature, or the moisture at the surface.
First: how long should germination take?
Before troubleshooting, make sure you’ve waited long enough. Some crops are slow by nature.
| Crop | Normal germination time |
|---|---|
| Radish, mustard, arugula, wheat | 1–2 days |
| Broccoli, kale, cabbage, kohlrabi, sunflower, peas | 2–3 days |
| Amaranth | 2–4 days |
| Beet, chard, basil | 4–6 days |
| Cilantro | 5–10 days |
| Parsley | 7–14 days |
If you’re within these windows, give it a little longer. For the full growing timeline, see how long microgreens take to grow.
The 9 most common causes
1. Old or poor-quality seed
Seed loses vigor over time, especially if stored warm or humid. An old packet might have 50% germination, or very slow, uneven germination.
Fix: run a germination test (below). Store seed in an airtight container in a cool, dark, dry place. Buy from suppliers who sell specifically for microgreens and sprouting, where seed turns over quickly.
2. The room is too cold
Most microgreens germinate best when the medium is about 65–75°F (18–24°C). In a cold room, germination can take twice as long, and slow seeds are more likely to rot or mold.
Fix: move trays to a warmer room or use a seedling heat mat during blackout only. Remove the mat once seedlings are up.
3. The surface dried out
Seeds sitting on top of the medium need constant moisture. If the surface dries for even a few hours during germination, the process can stall — and partly germinated seeds may die.
Fix: keep the tray covered during blackout and mist daily when the surface looks dry. See how to water microgreens.
4. The medium is waterlogged
The opposite problem: seeds sitting in soggy medium run short of oxygen and can rot before they sprout. You may notice a sour smell.
Fix: moisten the medium like a wrung-out sponge before sowing, and make sure trays drain.
5. Poor seed-to-medium contact
Seeds that rest loosely on lumpy soil or on top of other seeds dry out and struggle to root.
Fix: level the medium before sowing, spread seed in a single layer and press it gently into the surface with your palm or a flat board.
6. Seeds buried too deep
Most microgreen seeds are sown on the surface, not buried. Small seeds covered with a layer of soil may not reach the surface.
Fix: sow on top and rely on the blackout cover for darkness and humidity. A very light dusting of medium is fine for crops like cilantro, but not necessary.
7. Soaked the wrong seeds — or soaked too long
Soaking mucilaginous seeds (basil, chia, mustard, arugula) turns them into a gel blob that’s hard to sow and can suffocate. Soaking large seeds far longer than 12–24 hours can also damage them.
Fix: follow the soak time chart.
8. Treated or processed seed
Garden seed is sometimes coated with fungicide, and grocery-store seeds and grains may be heat-treated, hulled or split — all of which can stop germination. (Split peas, hulled sunflower kernels and pearled barley will not sprout.)
Fix: buy untreated, whole seed sold for microgreens or sprouting.
9. Naturally slow or dormant seed
Some crops, like cilantro and parsley, are slow and uneven even with fresh seed. Beet and chard “seeds” are actually clusters with a hard coat.
Fix: be patient, soak beet, chard and cilantro for 4–12 hours, and use split cilantro seed for faster results.
How to run a germination test
This takes a few days and tells you whether the seed or your growing conditions are the problem.
- Count out 20 seeds.
- Place them on a damp paper towel, fold it over, and put it in a zip bag or container.
- Keep at room temperature (around 70°F / 21°C).
- After 3 days (5–7 days for basil, beet and cilantro), count how many have sprouted.
- Multiply by 5 to get a percentage.
| Result | What it means |
|---|---|
| 85–100% | Seed is good — the problem is your setup (moisture, temperature, contact) |
| 70–85% | Usable; sow a little more seed to compensate |
| Below 70% | Replace the seed |
Our seed density guide explains how to adjust seed amounts for lower germination rates.
Patchy germination: what the pattern tells you
| Pattern | Likely cause |
|---|---|
| Good at the center, poor at the edges | Edges drying out — mist edges more, or cover better |
| Good at the edges, poor in the center | Center too wet, or seed piled up there |
| Random bare patches | Uneven sowing or lumpy medium |
| Uniformly sparse | Old seed or wrong seed amount |
| Strips or lines | Watering wash-out, or the medium wasn’t level |
Frequently asked questions
Should I uncover microgreens if only some have sprouted?
Once most have sprouted and are about an inch tall, uncover. Late seeds rarely catch up and the rest of the tray suffers if kept in the dark too long.
Can I reseed bare patches?
You can, but the new seedlings will lag far behind. It’s usually better to harvest what you have and adjust the next tray.
How long do microgreen seeds stay viable?
It varies by crop and storage. Many brassica seeds stay good for a few years in cool, dry storage, while others decline faster. A germination test is the only reliable way to know.
