How to Thin Seedlings (& Get Microgreens!)

Last Updated on December 28, 2022

Have you planted all your garden seeds, and now they’re starting to sprout? That’s excellent! This also means it will be time to thin them soon. As painful as it may be, it is best to thin your seedlings down to the one healthiest sprout per cell space or container after the first couple sets of true leaves appear. Thinning is a very important step in the seed-starting process to result in the most healthy, successful plants possible! They will thank you with explosive growth!

This post will discuss several methods of thinning, their pros and cons, what to do with the thinned seedlings, and other best practices. A thinning demonstration video is included at the end! If you’re interested in tips for starting seeds, read more here.

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Why thin seedlings?

When left un-thinned, seedlings that are in tight quarters will compete with one another for nutrients, water, air, and root space. Those are not things you want to deprive your seedlings of! In addition to concerns about competition, crowding seedlings also increases the risk for disease. This is primarily due to the reduced airflow between the plants. Bad guys like powdery mildew love cramped conditions, and also spread spores when leaves rub against one another. All of this applies to seedlings (or plants) that are started indoors in containers, and outside in the garden.

When to Thin Seedlings

It is best to wait until a couple weeks after sprouting, once the plants have developed a set of true leaves or two, but to not wait too much longer after that. The “true leaves” are the ones that emerge after the first set of sprouting leaves. Those very first ones are the embryonic leaves, called cotyledon, and are often times heart-shaped and indistinguishable between different types of plants. The true leaves more closely resemble what the mature plant leaves will look like, but miniature. Once a few of those pop, it helps you scope out the best looking seedlings.

When it comes time to thin, you get to choose the strongest, healthiest, best-looking seedling to keep around. After thinning, the chosen keepers will take off and thrive! Seedlings can quickly become four times the size of the ones that were left unthinned, in just a matter of weeks! Leaving them un-thinned stunts their development immensely.  I have experimented and experienced this first hand, numerous times!

HOW TO THIN SEEDLINGS

Like many aspects of gardening, this is sort of up to personal preference… but here I will share the two methods we primarily use: trimming, or gently separating apart.

A third option is to pull up on the unwanted seedling, manually plucking them out of their container – sometimes with the hopes of keeping the pulled seedling to replant. We do not use or encourage this practice since it can be a bit risky. Not only might the roots of the pulled seedling get damaged, thwarting your efforts to save it, but the seedling you are hoping to save and leave behind in the container may get damaged or completely pulled up along with it.

Thinning Seedlings by Trimming

Our preferred method to thin most types of seedlings is to trim out the unwanted ones. We simply snip off the smallest, thinnest, or leggiest ones at the root line with small sharp trimming scissors, leaving the chosen one behind.  We really love these trimming scissors and have several pairs! They’re frequently used on this homestead for many projects.

This is how we thin pretty much all of our vegetable seedlings, whether started in containers or directly sown outside. Aside from trying to reduce potential damage, we also just don’t have the need to save the excess ones. With limited space in the raised garden beds and under the lights in the greenhouse, what the heck would we do with all those additional salvaged plants? We already start more than we intend to grow, as extra insurance.  We do not have room for dozens more tomatoes, peppers, or squash on top of that.

Benefits of Trimming:

By cutting instead of pulling, it prevents accidentally distributing the one you’ve chosen to keep – the strongest and thickest looking babe. Since we are not attempting to keep the ones we have thinned out by trimming (as you may do if you are separating them, discussed below), there is no need to pot up or plant out anything at the same time. This makes the thinning process via trimming very quick and easy! All we have to do is snip, and move on.

Note that we also start most of our vegetable seedlings in 4” pots or large cell 6-packs (as opposed to tiny peat pellets or smaller cell packs) which also reduces the urgency to pot them up early. This makes trimming even more appealing for us, as the plants do not need to be fussed with for any reason at the time of thinning. The plants will all be happy in their homes for quite a while, especially after they are thinned.

Potential Drawbacks:

Some people view the loss or “death” of these extra seedlings as a negative thing – an overlooked potential of future plants, or even as a waste. But we do not view it this way! Here is why:

Microgreens!

The ones we cut aren’t “going to waste” just because we don’t replant them! The thinnings are nutrient packed micro-greens. We eat them. Or most of them at least.

Which seedlings are edible? So many types! For example, any baby greens like lettuce or kale, other brassicas like broccoli or kohlrabi, or basically any veggie that you could otherwise eat the foliage of – are edible microgreens!  You will find a more complete list below.

These make for an excellent salad or meal topper! We use them mostly raw but can be cooked as well. They also make for a super high-class chicken treat. After cutting them, microgreens stay most fresh and crisp if refrigerated inside a sealed container, like a glass tupperware or ziplock-type bag, with a tiny splash of water in with them.  

Here is a list of edible seedlings,
and also those you want to avoid consuming

Thinning Seedlings by Separating

Another method used to thin seedlings is by gently separating them. To do this, carefully remove the whole chunk of soil, seedlings and roots out of their small container. You can usually accomplish this by by gently tipping the container on its side and easing the mass out, pushing up from the bottom as needed. Do not pull up on the seedlings themselves!

Gently break up the soil and pull the seedlings apart. As much as possible, take care not to forcibly rip the roots apart if they’re tangled together. Next, either immediately re-pot the ones you want to keep, or get them planted outside – but only if they’ve been hardened off first! (Post coming on hardening off next week!)

I use this method most often for flower starts, like sunflowers and zinnias. In my humble opinion, there is alwaaaaays more room for flowers in the garden! Especially zinnias, because they’re a monarch favorite! So I like to try to keep as much of those babies alive as possible. They’re usually pretty hardy and can handle this treatment. Also, we usually plant out flowers a bit earlier and smaller than our veggie starts. This means that when I separate them, I can plant them straight outside right then, not needing to repot them. We also do this with fava beans. The tomatoes and peppers need to be babied in the greenhouse for a bit longer.

Benefits of Separating:

One benefit of pulling apart seedlings is that you can exponentially increase the number of plants that you are keeping.  You could also potentially increase the number of plants that you’re able to start in a smaller space.

For example, if you only have one small shelf and grow light, you could fill one tray with six 6-packs. By using the trimming method, cutting them down to just one plant per cell, the result would be 36 plants. But if instead you separate out the multiple sprouts from each cell, you could easily end up with over a hundred plants! That is a lot of bang for your buck. However, once you separate them, they do need to go somewhere. That leads us to the potential con of this method:

Potential Drawbacks:

When you separate out seedlings, but it’s not yet time to plant them outdoors (e.g. they’re still too young and tender, you haven’t hardened them off yet, or there is still risk of frost) then they’ll need to be potted into individual containers. If we are following the previous example, now what are you going to do with 100 individual containers? Even if you have room for all those in your garden, do you have space and light to keep them happy in the meantime – until they go outside?

Another drawback of this method is the time that it takes. If you need to either pot them all up or plant them all out at the same time as thinning, it makes the process of thinning much more labor-intensive. This can make you less eager to get the task done and procrastinate on thinning, which isn’t in the best interest of the plants! I have felt this way several times, and feel similarly about potting up.

The final potential issue with this method is the risk of harming the plants. As long as you’re gentle and separate them early, many plants do okay with some root disturbance. They usually will not die, even if handled a bit rough. But when I do have to get rough with them, I can’t help but think “How would they have done if I hadn’t torn them apart like that?… Would they be even larger and more robust?”, especially if the plants are doing just so-so out in the garden later. Because while they may not die, root disturbance can cause a slight shock and setback in development.

Some plants have a super sensitive, delicate root system, and do not like to be disturbed at all.

These are ones that should not be thinned using the separation method. They should either be started directly outside in their final destination (called direct-sowing) or use the trimming method to thin them instead.

The following plants do not like to be transplanted, or are sensitive to root disturbance:

• Beans – direct sow preferred, though early gentle transplanting can be successful
• Nasturtiums – direct sow preferred
• Carrots – only direct-sow in place
• Radishes – only direct-sow in place
• Squash and Zucchini – okay to start indoors, but do so in a large enough container that they will not become root bound, and transplant out and/or pot up before they do
• Beets – same notes as squash
• Spinach – same notes as squash
• Peas – same notes as squash
• Melon – same notes as squash

Alright folks! That is the low-down on thinning seedlings! My thoughts and experience with thinning seedlings, that is.

So, whaddya say? Are you feeling a little less nervous about the situation, and ready to go snip off (or separate) some babies?!? Baby plants, I mean…

If it was time to thin your seedlings, it may also be about time to fertilize your seedlings for the first time too! Check out this post all about how, why, and when we use seaweed extract to fertilize seedlings. It is a gentle, sustainable, and effective multi-purpose organic fertilizer. We love it, and so do the plants!

I hope you found this helpful! If so, share it! Feel free to ask questions in the comments below.