What To Do After Seeds Sprout (6 Important Steps)

It’s exciting when seeds start to break through the soil and show signs of life! However, germination is only the beginning for a plant.

So, what should you do after seeds sprout? After your seeds sprout, remove any covering to prevent overheating, ensure adequate light, and promote good air flow. Use the right growing medium, and give seedlings water & fertilizer as needed. Thin your seedlings before transplant if needed, and harden them off to prepare them for the outdoors.

Remember that some seeds (such as carrots) should be planted outside, directly in the soil. For these direct-sown crops, you won’t need to transplant.

In this article, we’ll walk through the steps you can take after seeds sprout to ensure that the seedlings grow into healthy plants.

Let’s begin.

(If you want a complete seed starting walkthrough with video and other resources, check out our seed starting course today!)

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What To Do After Seeds Sprout

After your seeds sprout, their needs change. Most seeds don’t need light to germinate, but seedlings do need light to continue growing after they emerge from the soil.

After a seed sprouts into a seedling, it will need light for photosynthesis to produce energy and continue growing.

The following steps are a good way to ensure healthy seedlings after seed germination:

  • Remove Covering
  • Ensure Proper Light
  • Use The Right Growing Medium
  • Avoid Excessive Moisture
  • Thin Seedlings
  • Harden Off Seedlings
row cover
After seeds germinate, remove any covering to give them enough light and air flow.

Let’s start at the beginning: removing any covering from the seedlings.

Remove Covering

You may have used a humidity dome to maintain proper moisture levels for your seeds. If so, it is a good idea to remove the dome after the seeds sprout.

According to the University of New Hampshire, a humidity dome should be removed right after the first leaves appear (this applies to both indoor and outdoor seedlings). This helps to avoid damping off (more on this later).

carrot seedlings
Remove covering right after the first leaves appear on seedlings.
Image courtesy of user:
Dwight Sipler via:
Wikimedia Commons: https://commons.

When you start seeds outdoors, it may be necessary to cover the soil to protect against foraging squirrels and other creatures (there is nothing wrong with doing this!)

However, be sure to remove the covering after your seeds sprout. That way, the seedlings can get the light they need to grow.

If you are still worried about pests bothering your seedlings after germination, you do have some options.

One way to protect individual plants is to use a cloche. A cloche is a clear plastic or glass cover that goes over a single plant.

water bottles
You can use the top of a plastic bottle (with the bottom cut out) as a cloche.

A cloche has several benefits, including:

  • Heat & moisture retention (it acts as a mini greenhouse, trapping heat from sunlight and humidity in the air and soil underneath it)
  • Light Permeability (it is clear, so light can get through so seedlings can grow)
  • Pest Protection (insects cannot get through the cloche to bother your plants)

Some cloches have vents to allow plants to breathe on warm days. If it gets too hot, you might be better off removing the cloche to avoid overheating plants (even at the risk of pest damage).

You can also use a wire cloche. It will not keep insect pests out, but it will deter animal pests while still allowing plants to get the light they need.

If you need to protect an entire row of plants, consider using a row cover. A row cover is made of a breathable material which lets light through and protects against cold, birds, and pests.

row cover
A row cover is another option to keep plants warm and protected from pests.

Row covers come in different lengths and widths. Depending on the type, they may allow more or less light to get through. Depending on thickness and material, they may retain more or less heat.

Ensure Proper Light

After seedlings go outside, they should get enough light from the sun to ensure proper growth. However, they might not get enough light from a windowsill when they are still indoors.

tomato plant 3-23-2021
Plants may not get enough light in a windowsill in winter or early spring.

In that case, grow lights might be just the thing to replace sunlight when starting seeds indoors.

The University of Minnesota Extension suggests using fluorescent lights for seedlings. LED lights are also an option – they are more expensive up front, but less expensive on an ongoing basis (in terms of electricity costs to run them).

You can learn more about grow lights for seedlings in my article here.

LED lights
LEDs are more expensive than fluorescent lights, but also more energy efficient.

If your seeds sprout in a dim-light area, move them into a bright windowsill (ideally south-facing) or under grow lights (or both). Otherwise, they will get tall and “stretched out” as they grow towards the light.

Once you put your plants under grow lights, keep a close eye on them. Check their height daily – some can grow by several inches per day!

When the seedlings get tall enough, raise the grow lights higher to allow more room for growth. This will give them space to grow into, and it will keep the top leaves from getting burned by bright light.

According to the University of Maryland Extension, aim to keep the top of the plants 1 to 2 inches from the lights. Of course, this may vary depending on the light source (they can be a little further away for brighter lights).

tomato seedlings
As your seedlings grow taller, move the grow light up to keep it above the tops of the plants.

If your seedlings are outdoors, you might be using a plastic tarp, 5-gallon buckets, or other methods to keep them warm at night. This is fine, but be sure to remove these coverings during the day.

That way, your seedlings can get some sunlight to produce energy (via photosynthesis) so they can continue to grow.

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Use The Right Growing Medium

If you sprouted your seeds in a paper towel and plastic bag combo, it will be necessary to put the seedlings into a growing medium after germination. Even if you used seed starting mix, remember that many such mixes have no nutrients added (your seedlings need nutrients to grow!)

paper towel
If you sprouted your seeds in a wet paper towel/plastic bag combo, you will need to transplant into a growing medium or soil at some point.

You may also need to repot seedlings after they reach a certain size (for example, tomato plants might need an intermediate size pot between the seed tray and transplant outdoors).

Either way, using the right growing medium is important for germination and for the health of seedlings after the seeds sprout. According to the University of Maine Extension, your best bet is to use a sterile soilless mix with a pH of around 6.2.

Soil from the garden is not the best idea, since it could contain insects or diseases from previous years that survived the winter. Established plants might be able to resist these diseases, but seedlings are more vulnerable before they get bigger.

repotting plants
Choose a sterile soilless potting mix to keep seeds and seedlings healthy.

Some soilless seed starting mixes have nutrients in them, but others do not. If not, you can add in some fertilizer to provide the necessary nutrients for seedling growth.

Clemson University suggests fertilizing seedlings when the first true leaves appear (the original leaves from the sprouted seed, called cotyledons, are not true leaves!)

They suggest using a water-soluble fertilizer during every other watering. Don’t use fertilizers that are too strong, and follow the directions on the package.

seedlings in seed tray
You can fertilize seedlings after the first true leaves appear, but don’t overdo it!

Otherwise, you could over fertilize your seedlings.

Avoid Excessive Moisture

Seedlings still need water, but excessive moisture can cause all sorts of problems. For one thing, too much water in the soil leaves no room for air.

Soil that stays too wet will suffocate seedlings by denying them air and by killing their roots (by root rot). In addition, excessive moisture makes it more likely that seedlings will suffer from damping off.

damping off seedling
Image courtesy of user:
INAKAvillage211 via:
Wikimedia Commons

Damping off is a plant disease caused by pathogens that kill seeds and seedlings. It is more likely to happen in cool, wet soil.

According to the University of Missouri Extension, you can use a humidifier to prevent seedlings from drying out.  ou can also use pans to water pots or seed trays from below. (You can learn more about bottom watering plants here).

A spray bottle can also help to keep seedlings and their soil moist without over watering.

Thin Seedlings

After seeds sprout, you may find that there are too many of them. Maybe the seeds got planted too close together, or maybe you planted some extra to ensure you had enough to spare.

tomtao seedlings
If you planted too many seeds too close together, it might make sense to thin them to prevent competition and get fewer (but stronger) plants.

Either way, it makes sense to thin seedlings to prevent competition between plants. It also makes sense if you have limited space in the garden – after all, you can only plant and harvest so much.

Thinning seedlings basically means removing seedlings so that the remaining ones are properly spaced. Choose the strongest seedlings to remain, and remove the rest.

Harden Off Seedlings

Some seedlings (such as carrots) do not transplant well, so they should be started outdoors. Other crops (such as tomatoes and peppers) do not like cold, so they are often started indoors.

Before transplanting these crops outside, it is a good idea to harden off the seedlings. This means helping them to get stronger by gradually introducing them to outdoor conditions.

tomato plant 3-14-2021
To harden off plants, gradually increase their sunlight exposure.

For example, instead of transplanting seedlings directly into the soil outdoors, you bring the pots outside for a few hours per day. Over time, you gradually increase their exposure to sunlight and other outdoor elements.

You can learn more about hardening off seedlings in my article here.


Now you know what to do with seeds after they sprout. You also know what to avoid to ensure healthy seedlings.

You can find a full seed starting guide here.

I hope you found this article helpful. If so, please share it with someone who can use the information.

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Jon M

Hi, I'm Jon. Let's solve your gardening problems, spend more time growing, and get the best harvest every year!

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