How to thin seedlings without killing them

To be successful as a home gardener you need to master the skill of thinning out seedlings without damaging – or even killing – your plants.

And even if it is fiddly work, the good news is that thinning out is a skill that anyone can learn and master. 

Here in this article you will learn three distinctly different ways to thin out your seedlings started indoors.

Each method serves a specific purpose and situation and when you master them all, you are set for greatness in your home garden.

Why should I thin or separate seedlings

The easiest answer is that you do not want your seedlings to compete for nutrients, water and light.

And by separating your seedlings you ensure that each seedling is given the best possible conditions to grow and develop.

The simplest way to avoid too many seedlings in a small space is to look for information about proper spacing requirements on the seed packet.

When should I thin out seedlings?

One of the first gardening courses I took taught me to thin out seedlings early. And by that we mean when the seedlings have no more than one set of true leaves.

The reason to thin out early is of course that the roots are not yet large enough to be intertwined as you prick out seedlings growing close together.

But for me, it is not always practical to thin out seedlings early. For one thing, available space can be a real problem if you have to give all seeds that germinate and sprout their own pot after just a few weeks. 

I often transplant seedlings that have grown 2 or even 3 sets of true leaves. An example would be the leafy greens we sow in grow bags.

The baby greens, lettuce, arugula (rocket), spinach, kale, and Swiss chard we plant is harvested for salads but also transplanted into our vegetable garden when there is space to fill.

And with seedlings at hand, we never have to wait for seeds to germinate in our vegetable garden bed. Instead we transplant seedlings at all stages of development to our outdoors garden bed. 

Over the years I have formulated three methods that work for me when dealing with crowded seedlings. And each method is used for a specific situation and purpose.

  1. Pricking out seedlings 
  2. Thinning out seedlings by division
  3. Cutting to save remaining seedlings

Pricking out seedlings 

Pricking out works great for young and thin seedlings at the early stages of development. We prick out many different seedlings ranging from densely sown basil to kale and Swiss chard.

Pricking out is most useful for separating seedlings that have no more than one set of true leaves.

When to prick out seedlings

Do not wait too long if you are planning to prick out your seedlings. Ideally, the thinned seedlings should have no more than one set of true leaves.

If you wait too long, there is a risk that the seedlings have intertwined roots.

Typically, in any given pot, you will have one seedling that is dominant and that is clearly the strongest seedling. There will also be one seedling (or more) that is weaker.

And if you try to prick out seedlings with several pairs of true leaves, you risk damaging the roots of the dominant as well as the weaker other seedlings.

How to prick out seedlings

Pricking out seedlings is more fiddly that difficult. There are however a few key points that you need to be aware of.

  1. Be organised: You need to have seedlings, pots, potting mix and tools prepared and ready. You want to work fast and not expose the roots any longer than necessary when you thin your seedlings.
  2. Make sure that soil is moist before you separate seedlings
  3. Hold seedling gently by one of the leaves
  4. Insert dibble or stick into soil and lift the seedling
  5. Do not pull the seedling, just guide it gently as you lift it from pot
  6. When seedling is lifted, plant in new pot and gently firm soil
  7. Water and place pot in location with no direct sunlight to minimize risk of transplant shock

As you can see in the video tutorial I often prick out the extra seedlings while leaving the remaining seedling in the original pot.

Thinning seedlings by division

I prefer thinning larger seedlings by division whenever it is possible.

And I use thinning by division a lot for herbs with a delicate taproot as well as garden vegetables where I plant more than one seed in starter pots.

When to thin seedlings by division

Coriander, or cilantro, fennel and dill are examples of herbs where thinning by division is safer than attempting to prick out the individual seedlings. Both herbs develop a deep central tap root and it is quite difficult to extract the roots undamaged.

Hot peppers like habaneros and ghost peppers as well as tomatoes are examples of garden vegetables where I deliberately over sow and then thin out by division.

The key is however that there is enough nutrients, water and light for all seedlings to thrive and develop.

And, of course, planting more than one seed per pot will greatly increase your chances of growing a healthy plant.

How to divide seedlings

Thinning out seedlings by division takes a steady hand and confident handling.

Follow these simple steps to ensure success.

  1. Get organized, get all seedlings, pots and tools ready
  2. Make sure the soil in your pots is moist before starting
  3. Place your hand on top of the pot, make sure the stems are sat in-between your fingers
  4. Turn pot upside down and catch seedlings in your hand
  5. Start from soil level and gently separate the stems
  6. Plant each separated seedling in a pot and water

If you find the written explanation hard to follow, click for a video tutorial showing the whole process.

Cutting seedling when there are too many plants

As a general rule, gardeners do not like to cut or snip a seedling that could develop into a plant. But there are times when it is a necessary evil. When we simply have to accept that we have planted too many seeds and there is no other choice than to grab our scissors and snip.

For me, there are 3 scenarios where I will cut or snip a plant without thinking about transplanting the plants. Continue reading below or look at our instructional video.

1. When there is one dominant and several weaker plants:

At times there will be one dominant plant and several weaker plants with small leaves that are not fully formed or show other signs of poor development and growth.

Here I will snip the weaker plants to ensure that the stronger plant gets all the energy it needs to develop and grow strong.

2. When plants are growing too close to be thinned

Especially with smaller seeds, it is easy to sow too many seeds in one and the same spot. The result is often crowded plants where one seed more or less germinated on top of another.

Here we look for and snip or cut the weakest plants level with the soil. Do not pull the plant. Pulling will risk damaging the roots of both plants.

Also, pulling is not necessary as the roots will die when there are no leaves to sustain the plant.

3. If seedlings are too developed, and there is a risk of killing both

Then there is the scenario where the plants have developed to a mature size, and transplanting one will risk hurting both plants.

This has unfortunately happened more than once when planting, for example, cucumber seeds in a container. One plant will grow too close to another plant, and the root systems will become one.

In this scenario, it is better to cut the weaker plant. All we can do is learn for the next time we start a plant from seed.

Thinning seedlings grown from seeds that are growing too close
Thinning out seedlings to give each seedling an individual pot or cell.

Mattias Magnusson: Hello, I'm Mattias, a passionate and experienced gardening enthusiast. I am the creator of, your guide to year-round herb and veggie growing. Let's simplify green living, no matter your space or location.