Starting seedlings can be a straightforward process, but as we keep them indoors under constant observation, we may start to notice issues like yellowing leaves, legginess, damping off, etc. It happened to me, too. I started some of my seedlings early, but the weather didn’t allow them to go into the ground yet. After nearly a month, some of the bottom seedling leaves were turning yellow, and I soon learned why.

The first leaves, also called cotyledons, generally start yellowing at the 3-week mark, when the second and third sets of leaves have fully developed. This is normal. However, yellowing of the true leaves is a cause for concern and a sign that your seedlings may be overwatered or need fertilizing.

Before we get deeper into why the bottom leaves on certain seedlings can go yellow, it’s important to make a few distinctions between the first set of leaves and the first true leaves:

First Leaves vs. First True Leaves – What’s the Difference?

The first leaves that emerge right after germination, are called cotyledons, also known as “seed leaves”. They look very similar for many plants that belong to the same family – radish, cabbage, kale, kohlrabi, or turnip seedlings can have a very similar appearance in their first week of existence.

Once the first true leaves emerge, it’s quite easy to tell them apart. The cotyledons will stay small, while the true leaves will start looking like a miniature of the mature plant, and you will easily be able to tell them apart.

Don’t mistake cotyledons for actual leaves, though. Cotyledons are part of the plant’s embryo. Once they grow and emerge, their role is to supply nutrition and help the seedling establish itself during its “baby” phase through the process of photosynthesis.

When the seedling has several sets of leaves, cotyledons are no longer needed. For most plants, this happens after 3 to 4 weeks. Depending on the seed variety, the cotyledons will start to yellow, dry out, and fall off, or they can persist on the plant for months to come. Either way, if the bottom leaves on your seedling – the ones that don’t look anything like the others – start yellowing, and you otherwise have a healthy plant, you really shouldn’t worry.

Overwatering – the Main Culprit for Yellowing Leaves

So what happens if some of the true leaves are starting to yellow? Is this irreversible? Is the plant dying? Yellowing true leaves is indeed a cause for concern, but your plants are trying to tell you something. Different signs mean different things.

The most common mistake new gardeners make is to literally “shower” their plants with too much affection – a.k.a. overwater. There’s not much room for error when watering small module trays and you can easily end up with soggy modules. What this does is drive oxygen away from the soil mix and suffocate the roots that not only need water but also need air to thrive.

When watering seedlings, it’s best to err on the side of too little water and not too much. Underwatering is easily remedied – your seedlings will appear droopy and soft and sometimes fall over, but they’ll recover and spring right back up as soon as you give them enough water.

I know it’s a scary thing to let your seedlings go thirsty, but waterlogging them could lead to fungal disease, yellowing of leaves, and permanent damage.

The size of your module trays can make or break your progress – too small and it dries easily, too big and you’ll run out of space in your grow room. After much trial and error, I found this size of seed starting trays perfect for starting most seedlings.

Could It Be the Lights?

It’s always best to give your seedlings the optimum amount of light that they need, although this is a difficult thing to figure out, especially when growing plants indoors. When we start to see yellowing leaves, we can’t help but wonder – are they getting enough light? I’m here to tell you that they probably are, especially when using good grow lights.

I’ve been using strong LED lights from Mars Hydro for a couple of years now with great success, and, if anything, I find them too strong. Fortunately, they’re dimmable, which is what I’d advise you to buy if you’re shopping for grow lights.

The signs of not enough light are leggy seedlings with ridiculously long stems – that’s very different from yellowing leaves. Some seedlings hate getting too much light intensity, and their leaves start looking waxy, rigid, and turn a dark color. That’s a sign that your seedlings may have been burned by a light that’s too strong.

Light is essential, and so is darkness – you should give your young plants at least 8 hours of darkness – but light and darkness not the issue here, so let’s explore other possible causes for yellow leaves.

Should You Start Fertilizing?

During their first month of life, just like a nutritious egg yolk, the seed components and cotyledons have enough nutrition to support plant growth. Any longer than that, and you should either transplant your seedlings outside, in well-amended soil or move them to bigger pots and start fertilizing.

Your cool weather crops should go in the ground at the 6-week mark, the very latest; otherwise, they can become rootbound or have stunted growth. Worry about fertilizing them only after they have been transplanted.

Your warm-weather crops, like peppers, chilies, tomatoes, eggplants, will most likely spend a long time indoors. Along with potting them on, if their true leaves are showing signs of yellowing, they probably need fertilizing.

Choose an organic NPK fertilizer that’s balanced in all three components (this one is a good organic option), and proceed with caution – dilute it at a quarter or half strength and don’t fertilize too often. Mixing one part potting soil with one part generic compost can also do the trick and slowly release the nutrients that your seedlings need.

Over-fertilizing can actually be more damaging to your plants than under-fertilizing. It can lead to stunted growth, susceptibility to pests and disease, and yes, even yellowing of leaves.

YouTube video
Video examples of cotyledons turning yellow.

Yellowing Leaves – Easy Fixes

When your seedlings get yellowing leaves, as long as they still have green, healthy growth, all is not lost. Here are the main things you can do to ensure that your plants recover and strengthen:

Snip the yellow leaves off.

Whether we’re talking about cotyledons or true leaves, when a leaf goes yellow and limp, it’s no longer serving the plant. Even at the seedling stage, some pruning will help the plant drive energy to the leaves that matter, not the dying ones.

With a pair of fine scissors, snip the yellowing leaves at the base of their stem and discard them. With cotyledons, you may notice that they will often fall off on their own – you’re just speeding up the process.

Check the weight of your trays.

One great way to learn if you’ve been overwatering is by checking the weight of your module trays when they’re dry and when you’ve just watered them. When watering, don’t just check for empty bottom trays. The seed starting mix acts like a sponge and can still hold a lot of water and this will translate into a heavier tray than usual.

Potting mixes that contain lots of peat – or its eco-friendlier version, coco coir – are excellent for retaining adequate moisture levels, and they become very light when water has evaporated. Check this article for a DIY coco coir seed starting mix.

When your trays are lighter and the top layer of soil is drying out, it’s time to water risk-free.

Go easy on the fertilizer.

Fertilizing is a personal preference for many gardeners. But if this topic is confusing to you – what kind of fertilizer to use, what concentration, how often, etc – then you can skip this step altogether. Your seedlings will still need nutrients after a couple of weeks, and they can access them directly from the soil if you’ve used the right soil mix that has organic matter in it, not just sterile peat or coir potting mix.

Many gardeners start their seeds in 100% compost, and I’ve done this myself successfully. The only thing to pay attention to is drainage – not all composts are created equal, and some will have better drainage than others. But just like all things in gardening, it’s a matter of trial and error.

Don’t keep your seedlings indoors for too long.

Quick-maturing crops and cool-season vegetables such as peas, lettuce, kohlrabi, kale, etc., thrive outdoors in the cold. You’re not doing them any favor if you’re keeping them cooped up inside the house, where it’s warm, and there are no stressors to strengthen them.

These plants might be showing signs of yellowing because it’s too warm inside, and it’s high time you transplanted them outdoors. Generally, 4 to 6 weeks is perfect timing for planting these seedlings outside, but you can transplant them even sooner, and they’ll adapt much faster than older plants.


As with all setbacks in gardening, if you get yellowing leaves on your seedlings, don’t panic. With a little care, they’ll most likely recover. But even if they don’t, even if you lose an entire batch of seedlings, it’s not the end of the world. Just start again. If you transplant a new batch outside when the seedlings are young, and the weather conditions are perfect, you’ll be shocked by how much growth you’ll get – often surpassing your older, more feeble plants.

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