How to Grow Microgreens in a Greenhouse: Step by Step

Growing microgreens in a greenhouse is the fastest path from seed to plate in all of horticulture. Most varieties go from dry seed to harvest-ready in 7 to 14 days, require minimal space, and produce more nutrition per square foot than any other crop. This how-to guide covers the complete process: selecting varieties, preparing trays, managing the blackout and greening phases, harvesting, and troubleshooting the problems that derail beginners.

Step 1: Choosing Varieties

Start with the five most reliable greenhouse microgreens: sunflower (large, crunchy, nutty), pea shoots (sweet, tender, long shelf life), radish (spicy, colorful, fast — 5 to 7 days), broccoli (mild, health claims, steady demand), and basil (aromatic, slow at 10 to 14 days but high value). These five varieties forgive beginner mistakes, germinate reliably, and produce consistently in greenhouse conditions.

Step 2: Preparing Trays

Use standard 10-by-20-inch propagation trays with drainage holes. Fill with 1 to 1.5 inches of pre-moistened coconut coir or seed-starting mix. Level the surface without compacting — microgreen roots need loose, aerated media. Mist the surface until evenly damp but not puddled.

Spread seeds densely — much more densely than you would for transplant production. For sunflower and pea shoots, pre-soak seeds for 8 to 12 hours before sowing. Spread soaked seeds shoulder-to-shoulder across the tray surface, pressing lightly into contact with the media. For small seeds (radish, broccoli, basil), sprinkle evenly and mist to settle them into the surface without burying.

Step 3: Blackout Phase

Stack trays 3 to 5 high with a weighted tray on top. The weight presses seeds into firm contact with the moist media, improving germination rates. The darkness simulates soil cover and encourages root development before shoot elongation. Maintain 65 to 75°F during blackout. Check daily and mist lightly if the surface appears dry. Blackout lasts 2 to 4 days depending on species — sunflower and pea need 3 to 4 days; radish and broccoli need 2 to 3 days.

Step 4: Greening Phase

Unstack trays and expose to light. The pale yellow shoots green up rapidly — within 24 to 48 hours they develop chlorophyll and begin photosynthesizing. Position trays where they receive natural greenhouse light (at least 100 to 200 µmol/m²/s PPFD for 10 to 14 hours per day). In winter, supplement with an LED grow bar. Bottom-water daily by filling the solid under-tray with 1/4 inch of water and allowing the growing tray to wick it up. Avoid overhead watering, which promotes mold and damping-off.

Step 5: Harvest

Harvest when the first true leaves appear (or just before, when cotyledons are fully expanded). Cut stems just above the soil line with sharp scissors or a clean knife. Harvest into a clean container and refrigerate immediately. Most microgreens store for 5 to 10 days in a sealed container with a paper towel to absorb excess moisture. Do not wash before storage — wash just before eating.

Troubleshooting

Mold (white fuzzy growth on the media surface or stem bases) is the primary problem. Causes: poor air circulation, overwatering, contaminated seed, or reusing trays without sanitizing. Prevention: run a small fan near trays, bottom-water only, sanitize trays with dilute hydrogen peroxide between batches, and use high-quality seed from reputable suppliers. If mold appears, remove the affected tray immediately to prevent spore spread.

Uneven germination means seed was spread unevenly, moisture was inconsistent, or seed quality was poor. Distribute seeds as uniformly as possible and ensure the entire tray surface is evenly moist before stacking for blackout. Old or improperly stored seed germinates poorly — buy fresh seed each season from a supplier that specializes in microgreen-grade seed.

Sanitation Between Batches

Disease organisms accumulate in reused trays, on bench surfaces, and in residual growing media. Between every batch, wash trays with hot water and a dilute hydrogen peroxide solution (1 tablespoon per quart of water). Scrub away all root material and growing medium residue. Allow trays to air dry completely before replanting. Sanitize the bench surface with the same peroxide solution. This 10-minute cleaning routine between batches prevents the mold problems that plague growers who skip sanitation.

Replace growing media for each batch — do not reuse spent microgreen soil. Spent media contains root exudates, decomposing organic matter, and fungal spores that create ideal conditions for damping-off and mold in the next crop. Fresh coir or peat-based seed starting mix ensures a clean, disease-free foundation for every planting. The cost of fresh media ($2 to $4 per tray) is trivial compared to the value of a clean, healthy harvest and the cost of losing an entire tray to mold or disease contamination.

Source seed from reputable microgreen-specific suppliers rather than garden seed companies. Microgreen-grade seed is tested for germination rate, purity, and pathogen contamination. Garden-grade seed may have lower germination rates and higher levels of seed-borne pathogens that cause problems in the dense, moist conditions of microgreen production.