If you’re growing pepper plants from seed for the first time, you’ve embarked on a long journey. It can take up to 12 weeks of dedicated care and attention until you’ll be able to transplant your seedlings outside. In the meantime, a lot of things can happen to your pepper plants.

I’ve started peppers in cold frames in previous years because I didn’t own a greenhouse or grow lights, and my windowsills didn’t get enough light. This meant starting them late in the season and transplanting them to their final location when they were still young seedlings. The downside to this method was a late harvest.

Later on, I invested in powerful grow lights, started my peppers and other heat-loving plants super early, and faced many problems that I wasn’t familiar with. None severely impacted the growth of my seedlings, but I wanted to understand what was happening nonetheless.

Here are the main pepper seedling problems I’ve noticed when growing peppers indoors:

  1. Spotty or late germination
  2. Helmet head seedlings
  3. First leaves (cotyledons) pointing up
  4. Yellowing leaves
  5. Leaves curling up
  6. Leaf edema (small bumps or blisters)
  7. Peppers flowering too early
  8. Stunted growth

Are you struggling with similar issues? Read on, as I’ll explain and analyze each problem in detail.

1. Spotty or late germination

Peppers are often slow to germinate, and this can happen for many reasons. Pepper germination has a lot to do with soil temperature, humidity, seed quality, and the age of your seeds.

Soil temperature: Ideally, you want your soil temperature (not air!) to stay between 70 to 85°F (21 to 29°C). You can accomplish this by heating your grow room or placing a heat mat underneath your trays or pots. Pepper seeds will not germinate under 55°F (12°C). Typically, the seedlings will emerge after 7 to 10 days, but if the conditions aren’t right, they won’t germinate for weeks, if at all.

Humidity: While pepper seedlings hate to be overwatered, the seeds need to be constantly moist as they germinate. Some gardeners even go as far as sprouting the seeds before planting them.

Seed quality and seed age: These two factors are closely linked because as pepper seeds get older, their germination rate dramatically decreases. You’ll want to buy your seeds from reputable companies that test germination rates every year before selling seeds. If the pepper seeds are older than two years, you won’t get much germination. However, you can still test your old seeds and try to sprout some of them to figure out their germination rate. Line the seeds inside a wet paper towel and place the towel inside a ziplock bag to prevent evaporation. Then, observe how many of the seeds are still viable.

2. Helmet head seedlings

Your pepper seedlings will look like they’re wearing a “helmet” of seed husk on top of their first leaves. Sometimes, the leaves manage to escape on their own, but most often, they’ll need your help.

You’ll probably notice two situations: the seed husk is stuck on one of the leaves, or the seed is completely obstructing the first set of leaves from getting out. This second situation usually kills that particular seedling.

What you can do is mist the seed husk and keep a dome on top for a day or two to preserve humidity and moisten the hard hull. Then, using your fingers or tweezers, carefully remove the hull, trying not to hurt the leaves inside.

In most situations, the tip of the leaves will break inside the seed husk but that’s okay. When the “helmet” head situation is more severe, the pepper seedling’s growth may be stunted.

3. First leaves (cotyledons) pointing up

This may also look like something’s wrong with your pepper seedlings, but before you worry too much, know that the next leaves usually grow normally.

The first set of leaves, known as the cotyledons, are not true leaves. Their role is to nourish and support the young plant through photosynthesis until the true, larger leaves emerge.

While I’m not a botanist and can only presume what’s going on, I have a few theories based on what other gardeners are saying as well:

  • some varieties like to “close” their leaves up at night;
  • they may need more light;
  • they may be overwatered, and this is their response.

4. Yellowing leaves

I’ve talked about this in another article, and the same explanations can apply to pepper seedlings. Now, there are two kinds of yellowing leaves:

  • Yellowing cotyledons – which is perfectly normal, and they fall off on their own;
  • Yellowing true leaves – a sign of more complex problems which you should address.

Pepper plants like well-drained soil and they don’t do well when overwatered. When waterlogged, pepper seedling roots may suffer from a lack of oxygen and yellowing droopy leaves are often a sign that the plant is suffocating through overwatering.

But yellowing leaves could also be a sign of poor soil nutrition or lack of nitrogen, since older pepper seedlings need to be regularly fed with fertilizer – such as fish oil, seaweed, compost tea, etc. I fertilize my pepper seedlings every two weeks with a weak worm casting concentrate.

5. Leaves curling up

You’ll often see your pepper seedlings’ leaves curling up. Curling leaves on peppers can mean a dozen things outside in the garden, but when the pepper seedlings are indoors, away from pests and harsh weather, there aren’t many explanations. Mostly, it just means the soil is too wet.

I’ve noticed this often, particularly in my hot peppers, while my bell peppers didn’t seem to be as affected. It’s not just the amount of watering that’s the issue but also the type of soil you’re keeping your pepper seedlings in. My chosen soil mix for this year hasn’t been so good with drainage or water retention, so my seedlings are either too wet or too dry. I’m planning to fix this when moving them to bigger pots.

6. Leaf edema (small bumps or blisters)

Overwatering can also cause leaf edema in your pepper seedlings. Leaf edema looks like small, white-ish bumps or blisters all over the bottom of the leaves. Often, they’re visible from the top of the leaves as well. Leaf edema and curling up often go hand in hand – the edema causing the leaves to curl and look unhealthy.

This condition isn’t bacterial or viral; it’s just the plant’s inability to process the amount of water it receives. While we all know by now that overwatering is bad, we can’t really know exactly how much water peppers prefer. It’s just not feasible to water them a few times per day in small amounts, so we often water them generously, once every couple of days.

These irregular periods of “floods” and “droughts” may cause edema on your peppers’ leaves. Leaf edema is mostly a condition that plagues indoor peppers. Add poor air circulation and low calcium in the mix, as they could also greatly influence the health of your plants.

The answer to leaf edema is to go easy on watering, harden off your pepper seedlings properly over the span of two weeks and plant them in the garden as soon as you can. They’ll recover.

7. Peppers flowering too early

My pepper seedlings are 7 weeks old. They’re tall and bushy and already setting flowers like crazy. The problem is, it’s way too early for flowers and even way too early for my peppers to go outside. They have one more full month of growing inside to go.

Flowering in peppers is usually triggered by a couple of things:

  • intense grow lights – I may have set my Mars Hydro lights too high, thus encouraging flowering;
  • small pots – the pepper seedlings no longer have room inside the pot for their roots, so they stop producing foliage and start setting flowers.

You have a few options when seeing flowers so early in the season. One is picking the flowers off. This is often a laborious and delicate process, as peppers tend to set many flowers continuously.

The second option is topping off your pepper seedlings. Gardeners often top off their pepper seedlings – a.k.a. cut the top off – to encourage branching and lateral growth. This results in sturdier pepper plants and better pepper production. But what this also does is encourage more foliage growth and later flower production. Most of the seedling tips you will be removing contain all the pepper flowers anyway.

I know that topping off any of your seedlings may seem scary if you’re doing it for the first time, but I guarantee you that in as little as 3-4 days, new growth will sprout and form branches, just like in the pictures below:

8. Stunted growth

All of the problems above, particularly late germination and overwatering, can cause stunted growth to your pepper seedlings. And if this has already happened, there’s not much you could do about it except continue to water them carefully and to feed them as needed.

The most important thing you could do to encourage rapid growth is to change the size of your pepper seedlings’ containers. Peppers grow to the size of their containers, and you can intentionally keep them small if you limit their roots to a confined pot.

But as soon as you give the roots more room and fresh new soil, you’ll be amazed at how quickly they’ll take off. I start growing my pepper seedlings in trays, and then I move them to bigger pots once they start growing their second true leaves. If I’m planning to keep my peppers in pots for 12 weeks before transplanting outside, they may need to be potted on even more, depending on their size.

You can check the state of their roots by gently pulling the pepper out of its container. If the roots are showing, and you’re not ready to plant them outside, you can move them to larger pots.


Growing pepper seedlings indoors isn’t difficult, but no matter how carefully you’re tending to your seedlings, you’ll inevitably face at least some of these problems, if not all.

Pepper seedlings have a clear way of showing when they’re struggling, but most of the time, they’ll recover. Even if some of their leaves look affected, remember that when transplanting, you’ll prune at least a quarter of foliage anyway. By doing this, you’re encouraging the plant’s energy to focus on establishing its roots rather than tending to sickly leaves.

I hope you’ve found some of the answers to your pepper seedling growing problems. Until next time, happy gardening!

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  1. Thank you so much, this was helpful. I am an experienced grower but have never had my pepper seedlings struggle so much to get true leaves. The cotyledons are all vertical as well. I changed up my seedling mix from peat based to coco coir (and perlite) so that is the only explanation. Maybe coir holds too much moisture. Everything else did great.

    1. Thanks for reading! I struggled with coco coir last year too, so I’m guessing it’s the quality of the coco coir itself, or something toxic they may be washing it with.

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