As an Amazon Associate, GrowJourney earns from qualifying purchases. Read more: terms of service.

Are your indoor garden seedlings weak, dead, or dying? In this article, you’ll find out what’s happening – and what to do about it.

You got excited about gardening so you got some seed packets. 

You brought your seeds home, plopped them in seed cells, and voila! You kill them all… assuming they even germinated in the first place.

If this sounds like you, please read on…

The days of killing your garden seedlings are about to be over…

Somewhere in our list of the Top 8 Ways To Kill Your Garden Seedlings you’ll find out what you did wrong AND more importantly, find out how to fix it.

Once you’ve mastered seed starting, you’ll be on your way to having a gorgeous garden and fresh, healthy foods with varieties you’ll never see at a grocery store.

Summer garden seedlings growing at Tyrant Farms.

Happy, healthy summer garden seedlings growing at Tyrant Farms.

The Top 8 Ways To Kill Your Garden Seedlings

The list below is in no particular order and sometimes you might have inadvertently used multiple methods on this list to kill your seedlings.

1. Damping Off


Your seedlings sprout and are looking great. Then one day, the stems go limp/wither and the seedlings start collapsing over on their sides. Death soon follows. You’ve just experienced “damping off.”


Damping off is a fungal disease caused by soil conditions being too wet and/or poor air circulation.


Prevention is the key to damping off. Once a seedling is infected, there’s no saving it. So prevent damping off as follows:  

a. If you use a domed seed starting tray, remove the dome as soon as your seeds have germinated.

b. Don’t overwater your seedlings. You want your seed starting mix to maintain consistent moisture, but not be wet. The ideal consistency in your seed starting mix is like a well wrung out sponge.

c. Try to keep your seedlings in an area with good air flow. If that’s not possible, consider getting a small fan to help.

d. Wash your reused seed starting trays and cells in hot soapy water. Also consider solarizing them (by putting them in the sun for an hour) before using them to kill any pathogenic microorganisms.

e. If a seedling or tray of seedlings gets damping off, immediately remove it from your seedling area to prevent further contamination of other seedlings.

2. Leggy seedlings 

Leggy, dying seedlings desperately stretching for sunlight.

Leggy, dying seedlings desperately stretching for sunlight.


Your seeds germinate and start growing. Rather than forming nice stocky seedlings with a proper leaf-to-stem ratio, they look like a toothpick with a tiny sprout on the end.

This is called having “leggy” seedlings. Eventually, the thin stems can’t support the weight of the leaves, causing the seedlings to collapse and die.


Too little light and/or not the right light spectrum. This makes your seedlings try to stretch taller as fast as possible to find sunlight, rather than grow balanced and healthy.


With modern, energy efficient windows, it’s very difficult to get enough light indoors to grow healthy seedlings – even in sunny south-facing windows.

There are three ways to avoid having leggy seedlings:

a. Use grow lights (here’s the DIY setup we recommend).

b. Direct sow your seeds outdoors.

c. Keep your seedlings indoors in front of your south-facing window but put them outside any day the temperature and weather permits. Example: if it’s sunny and over 50 degrees, you can put your summer seedlings outdoors in direct light, being careful not to let them get sunburned if they’ve never been exposed to direct light before (*see #8 below).

3. Improper Temperature


You did everything right and kept your seed starting mix moist, but your seeds never germinated. Assuming the seeds were still viable, you likely didn’t have them in their ideal germination temperature range.


Seeds are like Goldilocks: they want the temperature to be just right. Ok, so maybe seeds aren’t quite as picky as Goldilocks, but they still have an ideal soil temperature range at which they germinate.

For instance, tomato seeds like 75-85 degrees. Guess what happens if you try to start tomato seeds in your 50 degree basement? Nothing – as in the seeds don’t germinate.

On the other end of the spectrum, if you try to start seeds like carrots or lettuce on an 85+ degree heat mat, you’ll probably have the same results: no germination – because they prefer cooler germination temps.


Be sure to look at the ideal germination temperature for the type of seeds you’re starting. If you’re trying to start heat-loving summer seeds indoors, you’ll get much better results with a seedling heat mat & thermostat (assuming you don’t keep your house at 80+ degrees).

4. Drowning


Plants need water, so you figured you’d drench your seedlings. Then all your seedlings died. Yes, plants can drown and you just drowned yours.


If you visit a body of water like a pond or lake, you’ll find quite a few aquatic plants there – some of which are edible. However, your garden plants are not aquatic plants. 

Garden plants’ roots require aerobic soil with lots of oxygen. If you put too much water in your seed trays, your seedlings’ roots won’t be able to breathe and the plants will drown to death.


Don’t overwater your seedlings. Remember: the consistency of your seed starting mix should be like a well-wrung out sponge – damp, but not wet. 

5. Fungus Gnats

Fungus gnat effects (left) and larvae (right). Garden seedlings.

Fungus gnat effects (left) and larvae (right).


Your seedlings were doing fine until a bunch of small flies (resembling fruit flies) started hovering around their soil surface. Over the course of 7-10 days the seedlings stopped growing and died.

Your seedlings were killed by fungus gnat larvae.


Fungus gnats are small dark-colored flies whose small, white-colored larvae live in soil and eat the roots of young seedlings before becoming adult gnats. They can reproduce and proliferate rapidly, inhibiting your seedlings’ ability to get nutrition, which can lead to death.

Fungus gnats are quite common outdoors as well, but in a healthy garden ecosystem there are usually plenty of above and below-ground predators to keep them from causing too much harm.


If you notice adult fungus gnats on your seedlings and the weather doesn’t permit you to put your trays outside where predatory insects can keep them in check, purchase beneficial predatory nematodes (which are applied as a soil drench). 

Predatory nematodes are microscopic predators that will make short work of the fungus gnat larvae chewing on your seedlings’ roots. They also work great to manage soil-dwelling garden pests like root knot nematodes. 

6. Poor Nutrition


Your seedlings sprouted fine but at some point they stopped growing and the leaves turned yellow. Your seedlings are malnourished.


Lack of nutrition.


Many seed starting mixes don’t contain fertilizer, compost, or worm castings.

7. You didn’t use seed starting mix


The soil in your containers/seed cells slowly turned into an impenetrable brick and your seedlings died. This is because you didn’t use seed starting mix.


You used garden soil instead of seed starting mix. Garden soil is too heavy to use for seed starting and will become compacted.


Always use a seed starting mix when starting seeds. Again, here’s our DIY seed starting mix recipe or here’s a good organic seed starting mix you can buy pre-made.

8. Sunburn


You’ve done everything right. Your seedlings are growing. It’s a nice sunny day outside so you decide to put your seedlings outside in full sun.

You check back later in the day and the leaves are wilted with a white papery look. You just gave your seedlings a serious sunburn. (*This will also happen if you transplant indoor-grown seedlings into your garden that have never been exposed to full outdoor sunlight before.)


The giant nuclear fusion reactor floating 93 million miles from earth, aka the sun. Imagine if you were living in Canada in the winter and then you went on vacation in Jamaica – would you get sunburned if you were outside for 6 hours straight with no sunscreen on?


“Harden off” your seedlings if they’re new to direct sunlight (yes, that includes seedlings grown under grow lights). Here’s a good hardening off schedule you can use:

Days 1 – 3: Place your seedlings outdoors in a shady spot that will only get 3-5 hours of direct sunlight throughout the day.

Days 4 – 5: Place your seedlings in a slightly sunnier spot that will get about 5-6 hours of direct sunlight.

Days 6 – 7: Place your seedlings in a full sun spot (6+ hours of direct sunlight).

Now you know how you killed your seedlings and what to do about it! If you want to learn more about starting gardening plants from seed, we have three free video classes and an ebook available here.

Happy gardening!

Sometimes our articles will contain Amazon affiliate product links. These products have been carefully curated by our team. We use them, trust them, and know they work (or in the case of books, know that the information is extremely helpful). GrowJourney may earn a small commission on any sales that are generated via these affiliate links (without any additional cost to you).