Why I Do Not Like Seeing Early Flowers on My Chili Seedlings – And What I Do About It

The plants in the image above are Aurora chili peppers. I started them indoors from seed toward the end of February and have kept them under grow lights ever since. We are now in the first half of May, and as you can see, they are not just flowering, they have already started fruiting as well…
These Early Flowers Look Great, But They Do More Harm Than Good
I still remember the first time I saw my chili seedlings flower. I was excited. It felt like they were ahead of schedule, thriving. But since then, I have learned that early flowers are not always a good sign.
In fact, I do not like seeing flowers and fruit on my chili plants anymore – at least not yet. Why? Because it is too early for that…
You see, these plants are still too small to be flowering and fruiting. I am still keeping them indoors. I am still growing them under grow lights as seedlings. And they will stay indoors for at least two or three more weeks – until the end of May, when the weather usually warms up enough to move them into the garden and into their final (much bigger) pots.
Now, the problem with early flowering and fruiting – when the plants are still in the seedling stage – is that they are spending energy on the wrong things. Instead of building strong roots and growing larger leaves and stems, they are using energy to produce flowers, and worse – fruit.

So it is basically a waste of energy. It slows down growth and can leave you with smaller plants and fewer peppers later in the season. I have seen plants stall completely after flowering too early. They stayed small and barely produced any fruit later on…
It is like putting a roof on before the frame is up – you are skipping the steps that hold everything together. And the same is true for some of the other vegetables too: tomatoes, bell peppers, and eggplants.
How I Get My Plants Back On Track
Obviously, I do not want to see any flowers and fruits while the plants are in their seedling stage. But it still happens. Sooner or later, they will start flowering no matter what you do. It is just nature doing its thing…
What is interesting, though, is if you are keeping them in a container that is too small for them, the flowering will happen even sooner. It is like their survival instinct kicks in the moment they feel they have run out of space. And of course, they do not know that I am planning to transplant them outside as soon as the weather conditions allow it.

So the real question is not how to stop them from flowering, it is what to do when you notice it is already happening. I do not have a definitive answer, but I can tell you what I do:
The Solution That Is Not Perfect, But Still Worth It
The first thing I do when I notice the first flowers forming is check whether there are roots poking out of the draining holes which means the plant has outgrown its pot:
- If the chili seedling has not outgrown its pot (no roots showing at the bottom), I just remove the flowers and fruit and let it keep growing.
- If it has outgrown its pot (roots poking out of the drainage holes), I repot it into a bigger container, and then remove all the flowers and fruit.
That way, the plants shift their energy back to where it matters: Into growing stronger roots, and larger stems and leaves.
It works because once they have no flowers and fruit, their natural response is to grow them again. But to do that, they need to become stronger first. So they go back to developing roots, growing more and bigger leaves, and getting larger overall. It is like rebuilding the foundation before adding anything on top.

The root-bound ones respond especially well to this. For them, moving to a bigger pot is also like stretching after a long car ride. It is stiff at first, then full of movement and life again. They love it. And their growth explodes soon afterwards.
It is not an ideal solution, though. Repotting takes time, especially if you need to do it more than once in a season – like I had to with these Aurora seedlings. I already repotted them once about a month ago (on April 9th), when they were smaller and had just started to flower. But so far, it is the only way I have found to keep them growing larger and stronger, instead of stalling out too soon.
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