How to Prune Peppers for Maximum Yield (growing indoors hydroponically)

Pruning peppers is a hotly debated topic. Personally, I believe in it!

I find that pruning peppers, especially in indoor hydroponic environments, creates sturdier more compact plants with higher yields. Here’s everything I’ve learned about how and why to prune peppers!



shishito pepper and jigsaw pepper plants in my indoor gardens


Pruning Peppers

Starting pepper plants is tricky, but once the seedlings have sprouted they tend to grow quickly and easily.

Since I’m growing entirely indoors, inside my Aerogarden and other hydroponic units, my main constraint isn’t time or the weather.. but space. Pepper plants can easily grow several feet high, so pruning is a great way to keep the plants as compact and bushy for as long as possible.

But even if you are growing outdoors, you may find it beneficial to prune your pepper plants.



Why Prune Peppers?

The growth hormone within a pepper plant is concentrated at the top of the plant.

You’ll often see a young pepper plant that looks quite tall and leggy, with a thin stalk and a cluster of leaves at the top of the plant. The base of the plant, especially the bottom 1/3, will look quite bare bones and spindly.

By pruning, you essentially cause damage to the top of the plant, which signals the plant to redistribute its growth hormone along the entire stem of the pepper plant in an effort to keep growing.

The result is a lower, bushier plant.



Results of Pruning Pepper Plants

Here’s an example of a pepper plant before and after pruning:


See how much more leaves and side shoots are on the pruned pepper plant?

The more leaves on a pepper plant, the more flowers it will create and therefore the more opportunities to create peppers!

Pruned pepper plants also lead to stronger stems. Instead of a tall, top heavy plant, a shorter pruned pepper plant will have thicker stems and more distributed leaf growth.

In fact, I like to prune my plants to create a Christmas tree like shape, when possible, so that the bottom portion of the plant still receives adequate exposure to my grow lights.



Benefits of Pruning Peppers

So, in short, I prune my pepper plants for several reasons:

  • stronger, healthier plants
  • more pepper production
  • longer life within a constrained hydroponic system



How to Prune Peppers

There are two ways to prune peppers:

For both methods, you’ll want to use a clean pair of sharp garden scissors, like these.




Topping is the most common method of pruning peppers.

With topping, you’re literally cutting the top of the plant off. The cut part of the top will end in a stump, and the plant will start to grow into a Y shape from the interior portion of the leaves, where the growth nodes are.




FIM is a newer method, and one that I learned from indoor cannabis growers ha.

Who knew growing hot peppers and weed were similar?

The FIM method is a bit less harsh than the topping method, and personally I like it better! It stands for “F*ck, I Missed!” lol. I guess whoever started the method intended to top his plant and cut slightly too high.

Anyway, with the FIM method, you achieve the same result of causing damage to the top of the pepper plant and encouraging the growth hormone to run back down the stem of the plant.

BUT you don’t halt the plant from growing back out of the main stem altogether.

The damaged leaves will actually grow back and recover with time!


Try both and see which method you prefer.



When to Prune?

When you’re growing peppers for the first time, it’s really exciting to see them grow and you may not know when is the ‘right time’ for the first prune.

Personally, I like to prune once there are 4 sets of leaves (not counting the cotyledons).


I don’t like to wait and allow the pepper plants to get too tall, because I want to keep them as short as possible inside the Aerogarden.

You can experiment and see what works best for you!



How Many Times Should You Prune?

I tend to prune quite heavily.

Growing in a hydroponic environment, especially with a system like the Aerogarden, makes it nearly impossible to kill your plants.

You’re feeding your plants with continuous water, nutrients and light (everything they need to thrive), so although a heavy prune may set the plant back a couple days to a week, they recover quite quickly.

So, I prune my pepper plants several times in the early stages of the growing period. Each time they take about a week to recover, then grow back bushier and more compact than ever.

You can watch my Youtube video on pruning peppers here to see!



Growing Peppers Indoors Hydroponically



Even if you’re growing outdoors, you may want to prune multiple times.

Pepper plants are pretty hardy plants. They can easily live for several years and keep producing peppers year after year, so they’ll do even better long term if you prune!

So don’t worry about the flowers you may see on a young pepper plant.

I ignore them and focus on creating a bushy, strong and compact pepper plant for the first ~60 days. I want to encourage the plant to set itself up nicely before concentrating on bearing fruit.



Tips and Tricks With Pruning

One thing I have noticed is not all plants are equal.

Some pepper plants take to pruning better than others.

For example, my Korean hot peppers and Albino bell pepper immediately took to the first couple prunings and started sending out tons of offshoots all along the base of the plant.

My Chinese ornamental pepper however, was a bit more stubborn.

It clearly wanted to keep growing tall and had to be pruned more often and more heavily to encourage growth along the lower half of the plant. Even still, it concentrate its leaf production towards the top of the plant.

So experiment and see what works best on the varieties of peppers that you’re growing!

A great place to buy unique and heirloom seeds is Botanical Interests.



Growing Peppers Indoors

Because you do set the plant back each time you prune, I highly recommend starting your pepper plants indoors, in a hydroponic system!

That way, you’re not restricted to weather and temperature and you can start your plants in the dead of winter. You’ll prune, create stronger more productive plants, and then you can transplant them outside at a much more advanced stage and see much higher pepper production!

I use an Aerogarden to grow my pepper plants indoors. 

Any of their models will work for starting pepper plants but I recommend the 9-pod Bounty model or 24 pod Farm model if you want to grow peppers entirely inside.

Other companies like the Click & Grow and Rise Gardens also make great hydroponic systems.

Plants grown hydroponically grow 5 times as fast as plants grown in soil, so you can prune away and get great results with your peppers!



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