How to Separate Seedlings


Just about every gardener who has grown plants from seed will encounter an ‘over-sown’ pot. The question then becomes, how can I separate these little seedlings without killing them? Well, I have been separating seedlings for years and have developed my techniques for seedlings in any stage of growth.

In this article I’m going to show you what tools and materials should have on hand before you get started, how to separate both small and more mature seedlings, and finally how to deal with transplant shock.

Why thin or separate seedlings?

Seedlings, and all plants for that matter will generally grow larger when they have more space. When we sow seeds, we generally sow more than one. This often results in several seedlings in a pot or cell. In order for the seedling to grow and thrive, we should thin or separate and pot-up the seedlings into larger pots.

Look to the picture at the top of this article for confirmation. It is of some cardinal flower seedlings that I potted up to larger containers. The seedlings were about 2-3 mm diameter all clustered together. I separated 12 of the best seedlings into their own pots that were 100 mm (4″), and within 4 weeks the seedlings were 50 mm diameter (2″).

Should you thin or separate seedlings?

The answer to the above question is almost always ‘yes’. But the method as to thinning or separating needs to be determined by your goals. If you only want one plant, then you should just thin the seedlings by pinching or pulling them from the pot. But, if you want to grow many of the seedlings that germinated, then you should separate that many seedlings (at a minimum).

What happens if you don’t thin or separate seedlings

If you don’t thin or separate seedlings, your plants will be small and stunted. The size your plants will grow to is mainly determined by the container they are growing inside.

If you are growing vegetables, not thinning separating seedlings will result in low yields and poor producing plants.

When should you separate seedlings

As a general rule, you should wait to separate seedlings until several sets of true leaves have developed. When a seed germinates, the plant is very fragile. Any damage to the small tender root, stalk, or cotyledon leaves can prove fatal to the plant. The presence of 2-3 sets of true leaves will indicate the whole plant is stronger.

Diagram of a seedling.

What are true leaves?

Shortly after germination it will produce roots, a stalk, and two small leaves known as cotyledons. The cotyledon leaves are from the seed embryo, and contain initial stores of food for the seedling. Cotyledon leaves will be of different form (shape and structure) than the ‘true’ leaves of a mature plant.

Echinacea seedling showing the ‘true leaves’ versus cotyledons

Tools and Materials

Most of the time you won’t need any special tools to successfully separate seedlings. However, sometimes it is necessary to help loosen roots. So, some handy tools to keep nearby are listed below:

  • Toothpick
  • Wooden pencil
  • Pocket knife
  • Disposable plastic fork
  • Tweezers
  • Pots filled with moist potting soil

Difference between small & big seedlings

Not all seedlings are alike! This goes without saying, but the methods you would use to separate and transplant small seedlings is different from larger, more developed seedlings. Small immature seedlings need to be treated with much more care, while larger seedlings can be handled, grabbed, and be treated surprisingly rough.

If you are unsure if you have immature or mature seedlings, the picture below should help you. When the seedling cluster is removed from a pot or container, if the soil freely breaks up and separates, then the seedlings are immature. You know this because the roots are not entangled much, and lots of the soil can freely fall down.

If you remove a seedling cluster from a cell, by pulling it from the true leaves and the entire mass comes out at once, the seedlings are quite mature. The roots will likely be entangled, but the seedling will be able to be handled in a much rougher manner.

How to separate Seedlings

Separating small seedlings and repotting without killing them

In general, small seedlings can safely be removed from their pots, separated, and potted-up into larger pots without significant harm. But you need to be somewhat gentle. I’ve compiled the following process that seems to work for just about any plant, be it tomato, flower, or tree.

Separating immature seedlings in starter cells, six-packs, or small pots

  1. Massage the walls of the pot/cell that contain the seedling cluster. This will help loosen the soil from the pot.
  2. Carefully slide the seedling cluster out of the pot. Gently pinch the true leaves with your fingers and try to pull the seedling cluster out. If you feel the plants moving but the soil isn’t, stop! Tilt the pot on it’s side and try again. If the plants still feel like they want to dislodge from the soil, then either tilt the pot somewhat upside down, or slide a knife between the wall and soil to try to slide the entire cell out.
  3. Gently pull seedlings from the cluster by holding the true leaves. To do so, gently pinch the true leaves and set them into your already prepared pots with moist potting soil and holes. It may help to break the whole cell in two before doing this step. With young seedlings without significant roots, you should be able to peel them away easily.
  4. Backfill soil into the pot with the seedling. It helps to tilt the pot at an angle so gravity helps hold the seedling in place. Then, sprinkle soil in the hole, and gently press it to the seedling. You don’t want to press directly on the roots. See my diagram below – this method really works.
    • Click on image to enlarge
  5. Place the potted up seedling in a shady location for about a week. This allows roots to reattach themselves to the soil.

If you are using a large container such as a milk-jug, then separating seedlings is very easy. Simply use a plastic fork to scoop out the seedlings. It helps to hold the true leaves with one hand while lifting the fork from underneath the seedling. This helps preserve as much soil/root bond as possible, which will in turn lead to faster re-establishment.

Separating mature seedlings

For mature seedlings, we can modify our separation process to be much rougher. Now, you still want to be gentle for separating seedlings. But you don’t need to treat them like they are some delicate structure.

  1. Remove the seedling cluster or plant mass from the pot.
  2. Use your hands to find plant junctions that may ‘give’.
  3. Pull plants apart by grabbing around the root crowns or stems. But take care not to crush the stems or root crowns. You may wish to use a pencil or toothpick to help loosen roots. I’ve found that you can use a decent amount of force to pull the plants apart though.
    • I’m being quite forceful here, pulling the root crowns apart.
  4. Repot the individual plants in larger pots with moist potting soil.
  5. Place the newly repotted seedling in a shady location for about a week.

Video guide to separating seedlings

Here is a detailed video on how to perform the process of separating seedlings.

The ‘hunk-o-seedlings’ method

For separating mature seedlings in milk jugs from winter-sowing, there is another method that works well if you would like to directly transplant seedlings to their final location rather than potting them up. It is known as the hunk of seedlings method.

Hunk-O-Seedlings method, with result.

To do this, you simply cut ‘chunks’ of seedlings out of the milk-jug. Doing so will preserve the soil/root bond, which minimizes or negates any effect from transplant shock. Then, simply plant the hunk of seedlings into it’s final location. You can come back and thin excess seedlings in about a week, or skip that step and just let nature sort it out.

Dealing with transplant shock

Any time the roots of a plant are significantly disturbed while actively growing, they will experience some form of transplant shock. Transplant shock can be fatal to a plant if it is placed in very hot weather or direct sunlight, as the roots may not be bonded to the soil, and are not as able to use nutrients or transport water to the leaves.

To minimize the effects and risk of transplant shock, place recently transplanted seedlings in shady locations for about a week after transplanting. This amount of time is usually enough for the roots to reestablish themselves.

Why seedlings may wilt after transplanting

Anytime we remove a plant from it’s pot or ground and transfer it to a new pot/location, we risk damaging, stressing, or even killing the plant. The roots of plants bond with the soil they grow in, and when we disturb this bond the roots can no longer transfer water or nutrients to the plant efficiently. This can cause newly transplanted plants to wilt.

The factors cause plants to wilt after transplanting are as follows:

  • How much soil is disturbed/removed from the roots. The more ‘naked’ the roots are, the more stressed the plant will be, and fewer nutrients and water will make it to the plant.
  • How much sun the plant receives. While it is true that most plants love full sun, this also puts a heat load on the plant. Since plants cool themselves through water evaporation through the leaves, this will make it more likely to wilt.
  • Heat. The hotter the temperatures, regardless of sunlight will also contribute to plants wilting after transplanting.

Find more gardening tips here

Joe Foster

Hi - I grew up outdoors in nature - hiking, fishing, hunting. In high school I got my first job at a garden center where I learned to garden and landscape. I've been growing plants from seed and designing native plant gardens for over six years. I hope to share some of my knowledge with you! Additionally I am a wood worker / DIY enthusiast. I enjoy designing/building projects (with hand tools when I can!). I hope to give you some tips and useful information!

Recent Posts