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Caring for seedlings started indoors

Ferry-Morse Home Gardening Blog | 2024

Seedlings growing in peat pellets in a seed starting tray

Seedlings growing in peat pellets in a seed starting tray

Whether you're a seasoned seed starter or a beginner, there's always room to learn more about caring for seedlings.

And we encourage home gardeners to start seeds at home because it’s an economical way to have a lot of control over what you grow and the outcome.

This article will cover seedling care from germination to hardening off. So, let's get into it!

Quick overview of germination

Germination is the stage where seeds imbibe moisture and warmth to start growing. But, in truth, getting a seed to germinate is probably the easiest part of the seed-starting process.

What's my seed starting window?

Your indoor seed starting window for a spring garden is six to eight weeks before your region's last frost date.

How long does germination take?

When conditions are right, germination can take a few days to a couple of weeks and it happens in three stages:

  • Imbibition: Seed takes up water, softens, and swells
  • Lag or interim: Seed activates physiological preparations to grow
  • Radicle and root emergence: Cells replicate, and the embryonic root—the radicle—emerges
Agronomist taking soil samples in a field with a bucket, soil-analyzer device, trowel, and clipboard

Germinated wheat seeds with a developing root system

Do I need to start all seeds indoors?

The answer is no because many seeds—like cucumbers and okra—grow better as "direct sow." And the best part is that seed packets provide this information.

On the other hand, some varieties take a long time to reach maturity. So, starting seedlings indoors makes sense for plants like tomatoes, peppers, and eggplants.

Our article about growing a plant from seed includes a list of root-sensitive seedlings and the easiest plants to grow from seed. So, be sure to check out the super-helpful information it offers.

And to learn more about germinating seeds, see our resources on seed starting, reading seed packets, and using grow lights and heat mats.

What happens after germination?

At this stage, the following things are happening:

  • Roots develop and absorb water.
  • Embryonic leaves (cotyledons or "seed leaves") sprout.
  • True leaves emerge after cotyledons.
  • The plant shifts from food stored in the seed to photosynthesizing light into energy.

Here's an interesting fact: Some cotyledons remain below the soil line, referred to as hypogeal seedling emergence, such as peas. Seedlings that emerge with cotyledons above the soil line are epigeal, like beans.

How do you care for seedlings after seeds sprout?

So, let's get down to business. What do you do when tiny green leaves are staring back at you?

There are two stages to caring for seedlings:

  • The first four to six weeks; and
  • The last one to two weeks before your region's last average frost date.

Let's get into it.

Top-down view of seedlings growing in small pots situated in trays

Top-down view of seedlings growing in small pots situated in trays

The first four to six weeks after germination

After a sufficient number of your seeds germinate, do the following:

  • Remove the heat mat if you used one for germination.
  • Remove the clear lid from your seed starting tray, and place it under the tray, so you don't lose it.
  • Give your seedlings plenty of light—natural, artificial, or both.
  • Monitor for moisture, noticing when pellets turn a lighter shade of brown, indicating they are too dry.
  • When needed, add water to the bottom of the watertight plastic plant tray.

It's pretty simple, right? Let’s continue.

Heat mat under a seed starting tray

Heat mat under a seed starting tray

How do you keep seedlings healthy?

It’d be a shame to germinate some excellent varieties only to have them decline and not reach maturity. But don’t worry because we’ve listed some great tips below to help you succeed.

Lighting for indoor seedlings

Lighting options vary from a sunny window to relatively inexpensive fluorescent bulbs to LED lights. The bottom line is that strong light helps true leaves photosynthesize energy for your seedlings. 

Most importantly, adequate light prevents leggy seedlings with weak stems from elongating towards a distant light source, and leggy seedlings generally don't perform well after transplanting.

Our grow light kit with a T5 bulb provides just enough and not too much light. And the cool thing about many grow lights is that you can connect them to avoid overloading your electrical outlets. Isn’t that super-convenient?

Seedlings under a grow light with a T5 bulb

Seedlings under a grow light with a T5 bulb

Should seedlings be watered every day?

Seedlings usually don't require daily watering. However, if you let the soil dry too much, your seedlings will start to droop, and you'll probably need a wetting agent to penetrate the waxy crust peat moss forms when it dries. Conversely, if you water too much, you could introduce fungal disease. 


Most soilless seed-starting mixes are sterile. So, as seedlings grow, you’ll want to give them a dose of chemical fertilizer. Dilute it to about half-strength and add it to every second or third watering.

A home gardener pouring liquid fertilizer into a white watering can to mix with irrigation water for plants

A home gardener pouring liquid fertilizer into a white watering can to mix with irrigation water for plants


For some varieties, the strongest seedling in each pellet should remain. Also known as culling, it helps to limit competition for sunlight, air, and nutrients. And the best part is it promotes root growth!

Seed packets provide thinning instructions. And most of us drop more than one seed into each peat pellet, pot, or cell, which we're supposed to do! However, when germination is robust, it can lead to overcrowding in trays and strips.

Herb seeds are generally more forgiving in that you can let them grow in a bunch. But for other seedlings, consider thinning them out.

Garden snips can help you cut directly at the soil surface, or you can gently pull them apart and transplant them carefully. Snipping with small scissors at the soil line enables you to avoid disturbing the seedling roots you want to keep.

Small garden snips next to a seed starting tray with culled seedlings nearby

Small garden snips next to a seed starting tray with culled seedlings nearby


Pinching is removing new growth on a plant to produce a desired shape. Consider pinching down plants that look or produce better with multiple stalks. Examples of seedlings to pinch include lavender, basil, peppers, and some flower varieties like marigolds.


Damping-off is the result of excessive moisture, causing harmful microbial growth.

As we mentioned in our article about houseplants, overwatering is one of the leading causes of poor plant performance and can kill seedlings. Please keep reading to find out how to identify, prevent, and treat it.

The symptoms are:

Here are things you can do to prevent damping-off:

  • Sanitize pots and tools with 10 percent bleach solution or Lysol
  • Use seed starting mix because it's sterile
  • Avoid wetting leaves
  • Water from the bottom
  • Don't allow plants to sit in water
  • Give plants enough space to have good air circulation
  • Sprinkle cinnamon on top of the soil after planting to discourage fungal growth

Here's how to treat damping-off disease:

  • Remove fungus manually
  • Make sure you're not overwatering
  • Provide additional air circulation, such as with a small fan
  • Remove diseased plants and pots
  • Spray with hydrogen peroxide
  • On larger plants, consider spraying with neem oil
Ceylon Cinnamon sticks next to ground cinnamon pouring out of a wooden scoop

Ceylon Cinnamon sticks next to ground cinnamon pouring out of a wooden scoop

The last one to two weeks before your last frost date

The final weeks of seed starting are the home stretch before transplanting your seedlings outdoors. During this phase, you might need to move seedlings to a larger container, and you'll want to acclimate them to conditions outdoors.

Potting up

When your seedlings start to outgrow their peat pellets, winter weather lasts longer than expected, or you started your seeds too early (we've all done it), the remedy is to pot up to a larger container.

Also referred to as "bumping up," it simply means moving a plant to a larger container. Potting up promotes healthy seedlings by giving the roots room to develop.

And a Tidy Tray can be super-helpful in controlling the mess produced during this part of the process because if it’s cold outside, you’ll probably be potting up indoors.

A Tidy Tray on a countertop holding two seed packets, a rooted plant in a green glass jar, a small stack of biodegradable pots, and a white ceramic container with potting soil and a trowel

A Tidy Tray on a countertop holding two seed packets, a rooted plant in a green glass jar, a small stack of biodegradable pots, and a white ceramic container with potting soil and a trowel

Refer to your seed packet

So, we already know that seed packets are pretty helpful, right? Well, it gets better because planting instructions on the seed envelope might even tell you at which height to thin or transplant seedlings. 

How do I know when it's time to pot up?

When it's time to pot up, you'll see:

  • Excessive roots poking out of peat pellets
  • Plants getting over three to four inches tall
  • Seedlings that met the height or size requirements listed on the seed packet for transplanting
  • Seedlings showing reduced vigor, indicating they are root bound
Different seedlings in peat pots on a light blue wooden table with the caption

Different seedlings in peat pots on a light blue wooden table with the caption "Pot 'em up!"

Selecting a container

Small pots are suited for seedling growth. And you can move peat pellets to peat pots and then to your garden soil or containers. The best part is that they are biodegradable pots. So, root disturbance only happens one time.

When potting up seedlings to larger pots, try to select a container that is not more than two inches in diameter larger, like small peat pots. And please remember press the soil below the edge of the pot to prevent water from running off the sides.

Some creative ideas for containers to pot up small plants in pellets are yogurt cups, Solo cups, and paper cups. The container also needs drainage holes.

Wash old containers because these pots can harbor pathogens, weed seeds, and salts from fertilizers. If used for other plants or purposes, clean and disinfect it with one part bleach to nine parts water. Learn more about disinfecting flowerpots.

What planting media to use

The most important thing to remember is to use a planting mix made for indoor seeds. Please avoid field soil because it typically includes pathogens and insects that can kill delicate seedlings.

Most potting mix is pest-free, pre-treated, and designed to provide aeration, drainage, and water retention. Soilless media can include:

Removing your plants from seedling trays with care

Removing seedlings from trays can range from simple to tricky. Most of the time, gently lifting the peat pellet is all you'll need to do; careful not to grab the plant by the stem. Remember to always handle plants by their root ball or leaves.

It's important to know that for self-watering seed starting trays with a water-wicking mat, the biodegradable coating on a peat pellet might stick to the bottom of the tray (the mat). Wet it a little if you encounter this problem and you'll have nothing to worry about!

Applying a wetting agent

A wetting agent helps water reach the root zone of seedlings by penetrating the waxy crust left behind by peat moss and wood particles after they dry. 

Specifically, it:

  • Helps water soak into the planting mix
  • Reduces surface tension and runoff
  • Aids in water reaching the root zone

The best part is that two of the best wetting agents are everyday household items you can mix easily into your irrigation water.

Add a drop of dish detergent or pour a little apple cider vinegar into your watering can and see the results! Here's a video that demonstrates how it works.

Are you seeing any black flies?

Unfortunately, fungus gnats are a common problem when growing seedlings indoors. Some potting mixes contain their larvae, which hatch and fly all over your home.

They aren't harmful, just a nuisance. The University of Nebraska-Lincoln Extension Service and Oklahoma State University offer strategies to control this problem. So, check it out!

Also, learn the difference between a fungus gnat and a fruit fly. Take it further by learning more about general pest control for gardening.

Fungus gnat perched on the edge of a green leaf

Fungus gnat perched on the edge of a green leaf

Hardening off period

Hardening off is acclimating indoor seedlings to the outside environment before planting them in outdoor beds or containers.

It helps prevent the following problems:

  • Sun scorch
  • Stem breakage
  • Transplant shock
  • Seedling failure

In truth, it's a super-critical step!

When should I start the hardening process?

About two weeks before the last frost date in your region is when your weather should start to show signs of warming up. You'll want to take advantage of lovely sunny days to start hardening off your plants.

Give yourself about two weeks to complete this process of helping seedlings along to become mature and productive outdoor plants.

Observe the weather and try not to set plants out on really cold or super-windy days, as they will need time to adjust to the sun, temperatures, and wind. A gentle breeze helps stems thicken, but a stiff wind might break them. 

Simply observe how seedlings perform and if conditions are too intense, adjust your approach accordingly.

How do I care for seedlings while acclimating them to outdoor conditions?

Here are the basic steps you'll want to follow:

  • Start setting plants out for a few hours at a time and then increase gradually
  • Water regularly, ensuring consistent moisture but allowing the soil to dry slightly
  • Fertilize at half-to-full strength with a balanced fertilizer about every other watering
  • Take advantage of warmer, sunnier days
  • Move plants back indoors at night

Also, pay attention to pest problems, like animals that devour tender greens. In addition to physical barriers, consider using horticultural oil and kaolin clay as harmless ways to prevent such problems.

Try not to worry if the fertilizer is lower on phosphorus (the middle number on fertilizer) because the other two macronutrients are more important.

We also recommend staying away from organic fertilizer at this stage because it relies on microorganisms to break it down, which aren't prevalent in sterile peat pellets or seed starting mix.

Should seedlings be in direct sunlight?

You'll want to acclimate your plants to the sun gradually.

So, we recommend placing your baby plants in a semi-shady spot and then slowly moving them under more direct sun, monitoring their health and soil moisture levels.

And don't forget that even if it's sunny outside, temperatures can drop below your plants' preferred range. In this scenario, you'll want to bring them indoors until conditions are favorable. For example, basil seedlings love full-sun conditions but won't thrive in temperatures below 50° F.

Also, remember that a warm spring day can turn into a chilly night that can harm some plants when left outside. Learn more by reading our article about sunlight.

Seedling care: You've got this!

Before you know it, you'll have done such an excellent job of nurturing baby seedlings that you'll have healthy transplants ready to set directly in your outdoor garden beds or containers.

Using our process and products makes starting plants super simple and increases your chances of having healthy transplants.

You might end up with so many new seedlings that you could host a seedling exchange with friends and neighbors. So, give our advice a go and let us know if these seedling care tips helped in the comments below!

And as always, we're available to help via our Gardener's Helpline®. So, please reach out if you need us!