Seed Starting Problems? Here’s How to Fix the Most Common Issues

Starting seeds indoors is exciting, until you run into seed-starting problems like leggy seedlings, moldy soil, or seeds that refuse to sprout. If you’re growing your garden from scratch, a few hiccups are completely normal, but most are surprisingly easy to fix.

In this guide, we’ll walk through the most common seed starting issues and the simple adjustments that solve them fast. Whether you’re dealing with damping off, yellowing leaves, or slow growth, you’ll find beginner-friendly tips that work with basic supplies—not fancy equipment.

Seed starting really is a learning curve, but once you understand what your seedlings are telling you, everything gets easier. And if you’re building your garden season after season, you’ll love exploring our full Gardening page for more growing tips and inspiration.

This post contains affiliate links. This will not cost you anything, but will help us offset the cost of running the blog. We only share products we use and would recommend to a friend. Thank you for your support! Click ‘HERE’ for more info.

Starting seeds is both fun and frustrating for beginners and veterans alike. It’s something that, in zone 5, is a must-do for some veggie plants; otherwise, our growing season would not be long enough for everything to grow.

I hope you find some of these common problems and troubleshooting tips helpful in your seed starting journey! If we’ve forgotten anything, comment at the bottom and let us know!

Why Seed Starting Problems Happen

Because why wouldn’t they, right?! When something can go wrong, it usually does, or at least that’s how it feels sometimes. Once you get past some of these common problems, your seed-growing experience will get better.

Most seed starting issues come down to three simple things: light, moisture, and temperature. They all need to work together in order for your seedlings to survive and thrive.

When one of these three things is off, seedlings struggle. The good news is that small adjustments usually fix the problem quickly.

Seeds Aren’t Germinating

If your seeds are not sprouting, the most common causes are old seeds, cold soil, uneven moisture, or planting too deeply. Seeds need consistent warmth and moisture to wake up and grow. Using bottom heat can make a big difference, especially early in the season. Soaking seeds, switching to fresh seed, and adding a humidity dome can also improve germination.

Some vegetable and herb seeds need a little extra help to germinate, especially early in the season. Using bottom heat like this heating pad can make a big difference for warm-season crops like tomatoes, peppers, eggplant, basil, and okra, which all prefer consistently warm soil. This was a game-changer for my pepper seeds when starting them inside

Soaking seeds before planting helps soften hard seed coats and speeds up sprouting. This works well for peas, beans, beets, chard, parsley, and cilantro, especially when indoor air is dry.

A humidity dome helps maintain even moisture for seeds that are slow or delicate during germination. Lettuce, celery, onions, leeks, and many herbs benefit from this added humidity. Using fresh seed is also important for short-lived varieties like onions, leeks, and parsley, which lose viability faster than others.

While most seeds do not need light to germinate, there are some that do! Common examples include lettuce, spinach, celery, and most types of salad greens. Many herbs also need light, such as basil, thyme, oregano, chamomile, and lemon balm. Some flowers fall into this category as well, including snapdragons and petunias.

If you have seeds that require light to germinate, you’ll want to have your grow lights ready before you start your seeds so they have the best chance of germination. There are so many different shapes and sizes of grow lights. I personally use shop lights and hook them onto a large seed starting rack, but sometimes you just don’t need that large of a setup.

Seedlings Are Leggy

Leggy seedlings stretch tall and thin because they are searching for light. This usually happens when the light is too weak or too far away. Move your grow lights closer to the seedlings and consider switching to LED grow lights. Lowering the room temperature slightly can also help slow stretching.

Although it is a really cool experiment for kids to see when plants grow toward light to show that they are searching for it, it’s really NOT good for your seedlings. It makes them weak and strains them. Make sure your seedlings are directly underneath your grow lights; they shouldn’t have to try to seek the light out or stretch to find it.

The second photo above shows my poor seedling that is so weak it’s flopped over. The stem is thin and stretched. At first glance, I would guess this little tomato needs water, but it is actually in need of some light! It was working too hard to get the light it needed that the stem got weak and couldn’t hold up the leaves anymore. Put some light on this baby, water from the bottom, and watch it come back to life (hopefully!)

Mold or Fuzzy Growth on the Soil

White or fuzzy growth on the soil surface usually means there is too much moisture and not enough airflow. This is especially common when using humidity domes for too long. This is a problem I had a lot in the first couple of years of seed starting. I didn’t think I was watering too much, so I didn’t know what was going on!

The culprit is airflow. When I added a little fan to my plant room, it was a game-changer. Not only does it strengthen your seedlings so they can prepare for their journey to the garden, but it also helps the soil dry out properly in between watering. It is so important that the soil doesn’t stay saturated all the time.

Removing the humidity dome once seeds sprout and improving air circulation are two easy things you can do to avoid mold on your soil. Make sure you water from the bottom of your trays and let the soil dry in between watering as well.

Seedlings Falling Over (Damping Off)

Damping off is a fungal issue that causes seedlings to collapse at the soil line. It thrives in wet conditions and dirty containers. Having mold in the soil can be a sign that your seedlings are in danger of this fungus because the conditions are primed for it in wet and stagnant containers.

To help your seedlings from this terrible fate, improve airflow by adding a small fan, and avoid overwatering. You can sprinkle cinnamon or mist diluted hydrogen peroxide over the seedlings to help clean up and fight the fungus. Always start with clean, sterilized supplies, so you’re not inviting a problem from the beginning of germination.

Seedlings Are Yellowing

Yellow leaves often signal overwatering, poor drainage, or a lack of nutrients. Cold temperatures can also stress young seedlings and slow nutrient uptake.

Let the soil dry slightly between waterings and make sure containers drain well. When you water your seedlings, water from the bottom and let them soak up as much water as they want! After a few minutes, pour out the extra water so your plants aren’t sitting in water.

Move seedlings to a warmer area if it’s too cold in the room, and fertilize lightly once true leaves appear so the leaves get as many nutrients as they need as they start to get bigger!

Leaves Curling or Crispy

Curling or crispy leaves are often caused by heat stress or inconsistent watering. Low humidity can also dry out tender growth. If your seedlings look dry or dehydrated, they probably are! Give them what they need: water.

You can also raise the grow lights slightly and check for hot spots. Water evenly and make sure airflow is gentle rather than direct. I love my oscillating fan so that there’s consistent airflow during the day, but no direct fan right on the plants.

Slow or Stunted Growth

When seedlings grow slowly, cold soil or weak lighting is often the culprit. Your seedlings should be directly under your grow lights. If that means you need to prop them up a little bit, then do it until they are taller. You don’t want them to reach for the light, even if it’s right on top of them.

Crowded roots in small containers can also limit growth and stunt growth later. Up-pot seedlings once roots fill the container. If you start seeing roots come out of your seed tray, this might mean the roots are outgrowing the container.

Seedlings Drying Out Too Fast

Seedlings can dry out quickly in small cells or warm rooms. Direct airflow can make moisture evaporate even faster. I know what you’re thinking: “You just told me not to overwater and to put a fan on my seedlings!” It is a delicate balance!

Bottom watering helps soil absorb moisture evenly, but if your seeds are outgrowing their seed-starting mix, make sure to move them up. Better soil can hold moisture more efficiently than seed starting mix. Switching to larger containers and softening airflow can prevent stress if your seedlings are too dry.

Make sure you’re checking your seedlings often to ensure they aren’t too dry. A fan on your seedlings can be so helpful, but you don’t have to have it really close to them, and it doesn’t need to be on all the time. Use it when needed and adjust when necessary.

Explore More Seed-Starting & Gardening Guides

If you’re learning how to grow a strong, thriving garden from scratch, you’ll love these helpful posts:

• Make your own Seed Starting Mix: A simple, beginner-friendly guide to planting, scaping, and harvesting garlic successfully.
• Starting a Small Garden: You don’t need a huge space in order to have a garden. Try a smaller garden just to get your feet wet or because you only have a little spot to work with.
• Starting Seeds Indoors: This guide is for zone 5, but can be adapted for any zone. We offer tips and tricks, plus must-have supplies for seed starting.
• Tomato Companion Plants: Learn which plants help tomatoes thrive, and which ones to avoid.
• Composting with Hardware Cloth: Turn kitchen scraps into nutrient-rich compost for your seed-starting mix and garden beds.

FAQs About Seed Starting Problems

Ready to Grow Your Best Garden Yet?

If you’re gearing up for a productive garden season, don’t miss our full Gardening page.
It’s packed with beginner resources, planting guides, troubleshooting tips, and homestead-friendly projects to help your garden thrive, no matter your experience level. If you have seed starting issues that we didn’t cover or tips that would help a struggling gardener, share them below!