Planting Germinated Seeds in Soil after Sprouting

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Starting seeds is such a fun and empowering part of gardening. And, planting germinated seeds in soil most likely easier than you might expect!

Child's hand holding sprouted pea seed over soil trays
Germinated pea seed ready for planting

(I especially love starting seeds in wet paper towels – have you tried my favorite method? I’d recommend starting there if not!

I’m delighted to share the method I use when transplanting germinated seeds to soil. Once the seeds sprout, you can just about effortlessly transfer them!

Let’s get started with some frequently asked questions about transferring sprouted seeds to soil from their mini greenhouses or baggies. Then we’ll get into the actual steps!

Hand holding sprouted pea seed over soil
Sprouted snow pea seedling

Should I plant germinated seeds root up or down?

Plant germinated seeds root down. Like you would visualize any plant, roots grow down and then the rest of the plant grows up and breaks through the surface. Make it easier on the young sprouted seed by planting the root side pointing down.

Of course, if you did it the other way or can’t remember, you don’t need to go digging up anything. Most of the time, seeds will figure it out as they grow and look for the sunlight!

Black bean seed germinated with root sticking out
Germinated black bean seeds

How long does it take germinated seeds to sprout through the soil?

The timing when germinated seeds sprout through the soil surface after planting depends on a few things. The type and size of the seed may impact its growth rate. Some seeds grow faster than others for sure. Also, factors like light, watering, and how deep you plant already-sprouted seeds can affect the timing as well.

Choosing Sprouted Seeds for Transplanting

(If you haven’t already, follow the steps on our original guide first, to get your sprouted seeds!)

TIP – Be sure to check your seed package or research the exact seed type for specific details and planting instructions.

First, check to see how many seeds have sprouted.

You can remove only those with roots emerging during your first attempt at planting sprouted seeds.

Leave the rest until they are ready.

How to Plant Seeds after Germination

Separating Rooted Seedlings

Germinating seeds in materials other than soil or mix often results in a sprouted seed that is fully accessible. But, sometimes not.

Cucumber seedling with roots embedded in paper towel
This cucumber seedling’s roots are embedded in the paper towel!

Keep in mind that sprouted seeds may embed their roots into the wet towels, coffee filters, or whatever you used.

While it might seem alarming at first, this is actually pretty easy to remedy. 

How to Separate Seeds with Roots Embedded in Paper Towel

When roots from seeds are embedded in paper, simply separate those with roots still attached to the paper.

  1. First, identify any freely rooted seeds that haven’t attached to the paper. Remove those gently and set aside.
  2. Next, look for the least entangled sprouted seeds. See if you can gently separate them from the paper and other nearby seeds’ roots.

    Bright red beet seedling still attached to paper by the roots
  3. Finally, use great care in separating sprouted seeds with entangled roots. Tear the paper a bit to separate.
    • It’s okay if it the roots remain embedded in it. Just do your best not to break or disturb the roots when separating.
    • If you must break some of the tangled roots, do it as far away from the seed as possible and cutting as little root as possible. Very gently cut or pull them apart while grasping the sprouted seeds and paper at the same time.
Germinated Marketmore cucumber seedlings
Beautiful cucumber seed germination (Marketmore)

Whew! If that wasn’t stressful, I don’t know what is!

But it’s all good – your seeds should recover just fine in most cases.

Now that you have successfully freed the sprouted seeds that embedded their roots in paper, the rest is easy.

Germinated beet seed ready for planting
Red beet seedlings over a tray of soil for seed starting

How to Transplant Germinated Seeds

Planting seeds after germination doesn’t take much time as long as you have your supplies ready, along with a plan.

This is the complete guide to transferring sprouted seeds to soil. Follow these steps after germination in a medium other than soil.

  1. Check inside the plastic bag or container to see if the seeds have sprouted.
  2. Prepare little containers with potting mix for planting sprouted seeds.
  3. Gently remove each seed from the material it sprouted in. (Use the detailed steps above for seed radicles embedded in paper.)
  4. Refer to planting instructions for your specific type of seed. Specifically look at planting depth so you know how deep to plant germinated seeds.
    • TIP – When in doubt, I plant germinated seeds about ½ to 1 inch deep, with larger seeds going on the deeper side.
  5. Make a small hole in the soil of the planting container that is the proper depth for your seed.
  6. Gently place the sprouted seed root facing down into the hole. It’s okay if some of the paper towel is still attached.

    Replanting germinated peas into soil
  7. Lightly cover the sprouted seeds with potting mix or your preferred soil.

    Cucumber seedling transplanted into outdoor garden bed
    • TIP – If the seedling is already tall or has some leaves, you may allow some of it above the surface.
  8. Water the newly transplanted sprouted seed completely.  

    Lemon seedling after transplanting and watering
  9. Place the seed container in a sunny spot or under some grow lights. Watch to see when it breaks the surface!

When germinating seeds indoors, you’ll probably first notice the roots emerging first from the seed.

Next, the stem and cotyledon break through. 

Transplanting Sprouted Seeds Outdoors

If you wish to plant sprouted seeds directly in your garden outdoors, that is entirely possible too!

Follow the steps above but just make sure to plant the entire sprouted seed below the soil surface.

This allows it to avoid sunburn and harden off naturally, as opposed to the more tedious process of acclimating young indoor seedlings and plants to the outdoors.

Planting sprouted pea seeds
Sprouted snow pea seeds ready for planting

Planting Seeds after Germination

Now that you know how to transfer germinated seeds to soil from baggies, you can definitely speed up your seed starting plans!

I hope I answered all your questions about how to plant germinated seeds. You might also like to check out our Google Web Story on 3 Simple Seed Starting Methods!

As always, please hit me up in the comments with your questions or any other tips you’d like to share.

And related sprouted seed gardening stories are always welcome as well!

By the way, this is a great seed starting activity for young kids who are just getting interested in gardening!

Happy Gardening!

03.15.23 – Updated to include link to gws.

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  1. Sprouted radish seeds do NOT grow in the garden! They flower and become leggy with a pathetic tuber when you did them up.

    1. Hi Lesley, thank you so much for sharing your experience! Many of the seeds we start are part of garden experiments and a journey of learning. Every gardener’s experience helps the greater good – thanks for weighing in! Happy gardening!

    1. Hi Tom, thanks so much for the positivity and taking the time to comment. So happy you can share in this wonderful hobby with your grandchildren. I have such fond memories of being little and growing a sweet potato in water with my grandmother and gardening with my mom. Both of my grandfathers grew wonderful gardens and I loved it. I am so happy to share my experience and hearing of the wonderful memories you are making too. Best wishes!

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