The best time to transfer seeds that are germinating in paper towels into soil is when you first see that little root tip making an appearance. The bigger the root gets the harder it’s going to be to get them into soil without damaging/killing them.

Germinated Pepper Seedlings

The leftmost seed has that little white root tip showing so that’s an ideal time to get it in soil because you can plant it exactly how you would a regular seed. Anything right of the middle seed is what I’d call over-germinated.

I let a few of my seeds stay in their paper towel prisons until they got pretty big so I could show you how I’d repot them.

Removing Seeds from the Paper Towel

Sometimes it’s possible to gently tug on the seed to get the roots to slide out if they’ve grown through the paper towel. But, the most pepper roots have little hairy roots growing up the sides which can be damaged by trying to pull them through.

Pulling on the seed head can cause the seed head to pop off and sometimes the roots will snap if you’re too rough with them.

A much better way to do it is to carefully tear the paper towel around the root and leave a small piece of it attached. It won’t harm the plant to pot it up with the paper towel attached to the roots as it’ll disintegrate fairly quickly in the soil.

Planting Long Rooted Seeds in Soil

Now for the tricky part – getting your seed into soil without damaging those delicate roots.

Sometimes you get lucky and the root will be pointing straight down and you can break out the skills you learned playing operation as a kid to carefully lower it down a hole in the soil while holding the seed casing with some tweezers. It helps to make the hole bigger than you would for a seed so the roots don’t snag on the way down.

More often than not, the roots will have curled into an awkward position. If that’s the case, I prefer to make a much larger hole in the soil  – more of a crater really, as if I’m planting a small root ball.

Plant Pot With Hole in Soil

Hold the seed with some tweezers by the seed case in position in the crater so that the whole thing will be covered once you’ve filled it in. Then, while still holding the seed in position start carefully filling in the crater around the roots.

Compressing the soil like you would if you were planting a seed could damage the roots so a good alternative is to give them a really good water. The water will help the soil settle into place around the roots. Stick your plant in a warm spot to dry out a bit.

Planting Seeds with Cotyledon Leaves Forming

Planting a Sprouted Seed in Soil

If your sprout has started to form the cotyledon leaves then you might have a hook shape where the leaves are pointing downwards in the same direction the roots go. You’ll still want to plant this with the roots pointing downwards. When a plant grows normally the leaves are in that position just before they break the surface and once they do, they turn the right way up.

The bend in the neck can make it a bit awkward to hold it from the seed but the roots and stem are delicate and touching them could damage them.

Be careful filling in the hole around the roots. Try and avoid breaking them or knocking them around too much as they’ve haven’t had much resistance while they’ve been growing so aren’t very strong.

With these more developed seedlings I bury them just below the surface so that the plant can strengthen up as it emerges.

Planting a Sprouted Seed in Soil

Like with the other over grown seedlings it’s better to not compress the soil as it could damage the plants. Instead, give it a really good water to help the soil settle around the roots.

Cross your Fingers

I’ve had plenty of seeds that have grown into healthy plants even though they’ve been over germinated so all is not lost!

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  1. Mack November 16, 2021 at 5:09 am

    Nice tuteral. Thanks for the advice as i learned to not over root them. Which i have done. Your way ismuch easier. Again thanks for taking the time.

  2. James June 6, 2022 at 7:48 pm

    You can also carefully trim the paper towel with scissors, leaving the piece that is attached to the roots to avoid damaging them.
    Planting the seed with a small piece of paper towel attached to the roots won’t hurt anything, and is often safer than trying to detach it.


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