Troubleshooting Common Indoor Seed Starting Problems
Many gardeners want to start their garden seedlings themselves indoors for a number of reasons: save money, more variety, to get a jump on the season. Yet sometimes things go wrong, and seedlings don’t do their best. This can make for weak plants that don’t perform well once out in the garden.
Here are six common issues found with seedlings started indoors and how to correct them.
1. Leggy Seedlings (Tall, Weak Stems)
Cause: Insufficient light or light placed too far away.
Fix:
Ensure grow lights are 2–4 inches above seedlings and adjust as they grow.
Use a light timer for 12–16 hours of daily light exposure.
If using a window, rotate seedlings daily, provide a reflective background and supplement with a small LED grow light.
2. Mold or Fungal Growth on Soil
Cause: Poor air circulation or overwatering.
Fix:
Use a small fan on low to improve air movement. This also strengthens seedlings as they hold themselves against the push of air.
Water from the bottom using a tray once seeds have sprouted. Setting seedling containers inside a shallow container of water and allowing them to wick up water as needed keeps the surface drier.
Ensure seed trays have proper drainage.
Sprinkle a thin layer of cinnamon on the soil—it has natural antifungal properties.
3. Seeds Not Germinating
Cause: Soil temperature is too low, or seeds need light to germinate.
Fix:
Use a seedling heat mat to maintain optimal germination temperatures (65–75°F for most crops).
Some seeds (like lettuce) need light to germinate—check the seed packet and avoid burying them too deep.
4. Yellowing Leaves (Nutrient Deficiency or Overwatering)
Cause: Poor drainage, compacted soil, or lack of nutrients.
Fix:
Use a lightweight, well-draining seed-starting mix (not regular potting soil or garden soil).
Fertilize with diluted liquid seaweed or fish emulsion or your favorite liquid plant food once true leaves develop (1/4 to 1/2 strength to start).
Avoid overwatering—soil should be moist but not soggy. Watering from beneath with trays is effective; allow the soil to dry out before adding more water to the trays.
5. Seedlings Falling Over (Damping Off Disease)
Cause: Fungal infection due to excess moisture.
Fix:
Improve air circulation and avoid overcrowding seedlings.
Water seedlings in the morning to allow the soil to dry slightly before night or use bottom watering techniques described above.
Sterilize containers before reuse to prevent fungal spores from hanging around.
6. Seedlings Not Growing After Sprouting
Cause: Lack of nutrients or root-bound conditions.
Fix:
If seedlings are in small starter cells, pot them up to larger containers once they have 2–3 sets of true leaves.
Ensure consistent moisture and a balanced fertilizer after the first true leaves appear.
Pot plants up before the roots begin to protrude from the bottom of the container. When potting up, transfer to containers with potting soil rather than inert seed starting mixes.
It can take practice to successfully get seeds from germination to ready for the outside world. Keeping an eye out for trouble and resolving it at first sign increases your chances of success.
If you need help with seed starting basics, download my free Seed Starting Essentials eBook! It’s five chapters of the essential components to germinating and growing strong seedlings indoors.
Your Friend in the Garden,
