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Your garden seeds have germinated… Now what? Keeping seedlings health isn’t as easy as it might seem. These helpful tips will help you do it right!

Keeping seedlings healthy after germination

If you’ve browsed our articles before, you might have noticed that we have lots of resources to help gardeners grow their own plants from seeds. These include:

If you’re planning to start garden seeds soon or you already have yours started, this article provides the basic steps you need to take to ensure that they stay healthy until transplant day. 

A kale seedling sprouting under a DIY home grow light system. Keeping seedlings healthy by GrowJourney

A kale seedling sprouting under a DIY home grow light system.

How to grow healthy seedlings – 4 key considerations 

1. Timing & temperature

For starters, make sure to read the instructions on your seed packet (assuming there are instructions)! If you don’t know how to read a seed packet or you’re trying to interpret seed starting lingo, here’s a helpful guide

Usually, seed packets contain a bunch of helpful info, such as:

  • when to start your seeds, 
  • how to deep to sow them, and
  • how many days from germination to harvest (days to maturity). 

In the wild, temperature and moisture “tell” plant seeds when to germinate. Each plant species is a little different. (A tomato seed isn’t going to germinate in your garden at the same time that a cabbage seed will.) 

Many new gardeners make the mistake of thinking they can grow any plant they want during peak gardening season (warm months). They then get frustrated when their pea plants get fried to death by summer heat. 

Again, be sure that you’re starting the right plants at the right time of year, whether you’re starting your seedlings indoors or direct-sowing them outdoors in your garden.  

2. Light & water 


After your seeds germinate, your seedlings will immediately need bright light. With seeds directly sown outdoors, you can rely on the sun to provide light.

Indoor seedlings will need grow lights or a south-facing window. Keep in mind that modern energy-efficient windows often filter out so much light that indoor seedlings won’t get enough sun. They’ll get “leggy” (tall and weak), eventually flopping over and dying. 

You can also take your trays of seedlings outdoors on warm sunny days and bring them back inside before it gets cold. Just be mindful of the need to “harden them off” to direct sun exposure if they’ve never been outside before. 


Overwatering can easily kill young seedlings just as easily as under-watering can. Your target moisture range: keep your seedlings’ soil as moist as a wrung-out sponge.

Do not let the seedlings sit in standing water or you’ll cause their roots to rot.  

3. Seedling/plant food 

We’ve detailed elsewhere why it’s essential that you use seed starting mix rather than potting soil or garden soil. (Espoma makes an excellent organic seed starting mix.)

Good seed starting mixes have fertilizer in them, so you won’t need to worry about feeding your seedlings right after they germinate. Usually, you transplant your seedlings outdoors after 6-8 weeks

Over this period of time, it’s highly likely that your seedlings will need 1-2 rounds of additional fertilization, especially if they’re heavier feeders. If your seedlings are growing slowly, looking stunted, or have leaves turning yellow, that’s a good sign that they need food now!  

We recommend an organic liquid fertilizer such as:

Dilute your liquid fertilizer of choice as instructed on the container and apply to your seedlings. 

4. Indoor & outdoor seedling pests

If you’re lucky, you won’t end up with indoor pest insects on your seedlings, but chances are you will. When growing seedlings indoors vs outdoors, you don’t have the predatory insect populations you need to control your pest insects.

For indoor seedlings, the most frequent pest insect culprits are aphids and soil fungus gnats. Outdoors, the culprits tend to be aphids or larger critters like snails, slugs, pill bugs (aka rolly pollies), cutworms, squirrels (they accidentally dig them up while searching for nuts), and rabbits.

Here’s how to take care of each these pests organically:

Aphids (indoors or out):

Possible control methods:

  • squish them (if you’re ok with it),
  • spray them off with a gentle spray of water,
  • use neem oil, or
  • purchase live ladybugs to eat them (indoors you can put the seed trays in a plastic bin and release the ladybugs inside the tub)

Soil fungus gnats

Fungus gnats are common outdoors, but are controlled by predators. Indoors with no predators, they can be a big problem. They look similar to fruit flies, and their larvae will eat the roots of your seedlings, eventually killing them.

Control methods: The best option is purchasing some beneficial predatory nematodes to water your seedlings with. When properly applied, the nematodes will eat all the fungus gnat larvae within about 10 days. 

Snails, slugs, and pill bugs

These pests are a problem outdoors. We hope you don’t have them indoors!

Control methods: Use beer traps. For serious infestations, use OMRI-approved iron phosphate baits like Sluggo. (Don’t use Sluggo Plus, which contains additional ingredients that can kill beneficial insects.)


Cutworms are a serious problem for outdoor seedlings, not indoor seedlings. They’re the larvae of a Noctuidae moths, that come out at night to feed on plants.

Unfortunately, they chew the first part of the plant they encounter as they crawl along the ground. This is usually the plant’s stem, so they chop the whole seedling down at the base, killing it.

Control methods: It sounds odd, but you can effectively stop cut worms by inserting a stick directly in the ground parallel to your seedlings stem. A stick roughly the thickness of a toothpick will do. (You can even use tootpicks if you want!)

The worms feel their way around the seedling’s stem, hit the toothpick and think the plant is too tough to chew through. Then they move on. 


If you have a serious squirrel infestation, fear not!

You can prevent squirrels from digging up your garden beds by laying a sheet of flexible wire fencing over the surface (pin it down on the corners with garden staples). The holes are large enough for your seedlings and plants to grow right through but prevent squirrels from digging.  


Rabbits can be kept out of your garden beds with flex fencing about 18″ tall, pinned firmly to the ground.  

Keeping seedlings healthy is easy once you know the tricks and have some experience under your belt. If you have any questions, please ask away in the comments section below!

Additional resources:

Want to learn more about starting your own plants and keeping seedlings healthy? 

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