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When to Thin Seedlings

Once your seedlings reach a certain size, they need to be thinned out to allow healthy growth. It can be sad to see some seedlings go. But, it will give the remaining seedlings room to spread out and up!

In this post, I’ll go over when to thin seedlings and how to do it. I’ll even give you some tips on how to utilize those thinned seedlings. Let’s dive in.

Woman holding seedlings ready for thinning. Knowing when to thin seedlings is an important part of indoor gardening.

Why Thin Seedlings

With small or finicky seeds, it’s a good idea to sow more than one seed in case one doesn’t germinate. Especially if you’re working with a small space, you’ll want a viable seedling in every cell.

A lot of times, those multiple seeds will all germinate. You’re then left with competing seedlings in one cell.

While all three seedlings in one cell may appear healthy at first, eventually the seedlings will contend for space. Seedlings will run out of room to spread roots, and this will eventually cause their demise.

They’ll also be challenged to receive enough water, nutrients, and light.

Thinning seedlings to one per cell will allow the remaining seedling to grow healthy and strong.

Thinning seedlings also helps with airflow around your seed-starting setup. It’s the best way to avoid mold growing on soil or plant leaves.

When to Thin Seedlings

You don’t want to begin thinning seedlings too early. In the same breath, you don’t want to wait too long. Luckily, there are some ways to identify the best time to thin seedlings.

Let’s go over the tell-tale signs.

True Leaves Present

Cucumber Seedlings
True leaves forming on cucumber seedlings.

First of all, take a look at your seedlings. Do you see true leaves starting to form?

True leaves are what come after the first set of leaves. The first set of leaves that pop up after germination are known as cotyledons.

Cotyledons often resemble one another, no matter the type of seed. They are usually heart or oval-shaped. They may even have the seed shell still hanging on.

After the cotyledons come the true leaves. These are the second set of leaves to appear. And, they will more closely resemble a mature leaf of that particular vegetable or flower.

Once you see that true leaves are present, it’s a good sign it’s time to thin seedlings.

Competing Seedlings

Seedlings under a grow light.

The next sure sign of when to thin seedlings is seedlings competing for space. Once seedlings are large enough to have leaves intertwining, they need to be thinned back.

This will allow one seedling to be able to take off, instead of two to three seedlings experiencing mediocre growth.

What you can’t see are the competing roots, and this will soon reflect in stunted foliage development.

That’s why it’s important to visit your seedlings often. They grow faster than you think!

How to Thin Seedlings

A starter tray of watermelon seedlings.

Choose the Healthiest Seedling

There are a few methods for thinning seedlings, either by using snips or plucking seedlings by hand. But, before you thin seedlings, you’ll need to identify the seedling you wish to save.

My advice is to always choose the healthiest seedling. This is often the seedling with the largest leaves and best coloring. That is a direct reflection of a good root system present.

Avoid seedlings that are leaning, appear weak, or look much smaller than other seedlings.

Thin Using Snips

The first way you can thin seedlings is by using snips.

Snips will have small pointed blades. They should be small enough to get around seedlings without damaging others. Avoid using bulky pruning shears.

Using the snips, make a clean cut level with the soil. This is the best way to remove seedlings without disturbing the root system of the remaining seedling.

The removed seedling’s roots will not affect the remaining seedling’s roots as it grows larger. It will simply grow around them. So, you don’t have to worry about getting those extra roots out.

Save your thinned seedling instead of throwing it away (We’ll talk about this shortly).

Thin by Hand

Using a spoon to help thin seedlings.

The next method for thinning seedlings is by plucking the seedlings out by hand. I don’t recommend this method if your seedlings are extremely crowded. What will likely happen is you pull up the roots of all the seedlings because they are so intertwined.

Thinning by hand should be saved for small seedlings that are spread out in the cell. The perk to this method is that it’s quick and convenient.

To thin seedlings by hand, make sure that the soil or seed starting mix is damp. This will help keep roots in place.

Gently grab the seedling between your thumb and pointer finger. Slowly pull the seedling from the soil. If the remaining seedling looks like it will be pulled up, stop immediately and use snips instead.

Remember – don’t throw that thinned seedling out, yet! Bring a small bowl to store thinned seedlings in as you go.

How to Use Thinned Seedlings

So, what can you do with all your thinned seedlings? After all your hard work growing them, you should at least be able to use them for something!

Thinned vegetable seedlings can either be used for compost or microgreens.


If you regularly compost fruit, vegetables, and recyclable paper, throw in your non-edible seedlings as well. At least they will go to a good cause – soil health!


Microgreens used in a salad.

Edible seedlings can be used as microgreens for salads or a fresh snack. Create a microgreen salad with lemon vinaigrette, or enjoy pan-seared chicken with a microgreen garnish.

If you would normally eat the foliage of the vegetable, it should be safe to eat in seedling form.

Here are some common seedlings to use as microgreens:

Avoid using foliage from nightshade family vegetables such as potatoes, tomatoes, or peppers. These can be toxic when ingested.

Frequently Asked Questions

Thyme seedlings.

1. Can I replant the seedlings I remove?

Since you’ll be removing most seedlings at the soil surface, you will remove the seedling from its roots. Therefore, it won’t be able to survive. That’s why I recommend utilizing them as microgreens while they’re fresh.

If you were to separate the seedling roots and all, you could potentially replant it. But, it’s possible that you could damage the remaining seedling’s roots in the process.

2. Can I leave more than one seedling in a cell?

Ideally, every cell should only contain one seedling. This prevents root-bound seedlings and stunted growth.

In the case that you are using large pots or trays without dividers, you could have more than one seedling. Just make sure that each seedling has the recommended spacing for that particular vegetable.

3. Can I begin thinning seedlings too early?

Yes, as I mentioned before, you should wait until seedlings have formed true leaves. If you thin seedlings too early, you could potentially thin out the healthy seedling in that cell. It’s hard to tell until the seedlings have formed their first set of true leaves.

Wrapping Up When to Thin Seedlings

Closeup of cherry tomato seedlings.

Learning when to thin seedlings will give your seedlings a better chance at healthy growth. It’s also a great way to get your hands on some tasty microgreens!

Thinning seedlings isn’t the only thing that keeps your seedlings happy. Check out our Seed Starting page on the website for more blog posts. We’ll help you through the whole process with product recommendations, plus guides on starting all kinds of seeds.