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Why Do Seedlings Turn Brown – 18 Possible Causes

Keeping seedlings alive until they are big and strong enough to move into the garden doesn’t always happen without challenges. Despite our efforts to provide the best care, issues require us to troubleshoot to determine how best to help the plant. Especially when seedlings start to turn brown, our immediate fear is that the plant won’t survive. So, why do seedlings turn brown?

Seedlings mostly turn brown to nutrient deficiency and lack of water. Transplanting seedlings too late can cause stunted roots and also lead to browning. Sunburned seedlings are also possible.

It can be concerning when you see brown seedlings, but most of the time it’s fixable while the plant is still early on its development. Read on to find out what may be causing your seedlings to turn brown.

Reasons Your Seedlings Are Turning Brown

There are plenty of reasons why seedlings turn brown. Have a look at the list below to see which cause you may be experiencing!

Damping off

If this is the first you’ve heard of damping off, it’s very common. Several soil-borne fungi cause it. Usually, pathogens thrive in humid, moist, and warm conditions. The fungi which cause damping off prefer wet, cold soil. It causes seeds to rot during germination.

The emerging seedling becomes discolored and dies quickly. The other symptoms of damping off are thin or wilting stems where the plant touches the soil, a mushy feeling or appearance, and gray, black, or brown spots where splashback from the soil remains on the leaves. You may notice other seedlings fail to emerge at all. Damping off is often avoidable.

Provide drainage

Ensure that seedling pots have at least one large drainage hole. If using a tray under seedling pots, do not let them sit in water. Drain out any excess water the plants do not take in.

Provide air circulation 

While seedlings enjoy the warmth, the moisture created can worsen conditions. Provide fresh air by cracking a window or using a fan at low speed, so the seedlings don’t get blown over. Avoid cramming too many plants into a small space.

Use clean pots

If using the same seedling trays and pots from the previous year, clean them thoroughly with a solution of diluted bleach, white vinegar, or just plain dish soap. Also, clean gardening tools and gloves. This will stop the spread of the offending fungi from surfaces onto seedlings, especially if you’ve had this issue before.

Use fresh soil 

Do not reuse soil to avoid introducing fungi to your seedlings. Fungi can live in soil from year to year. Some brands sell sterilized potting soil. 

Provide warmth

Since the pathogens that cause damping off like cold soil, increase temperatures by using a heat mat or germinating seeds in the warmest place you can provide. You can try placing seed trays on the fridge or under a humidity dome. Do not water seedlings with very cold water.

Water from below 

It’s easy to oversaturate soil when watering from above. Keep a tray underneath seedling pots so that you can water at the base of the pots. This way, the soil will absorb only the amount of water needed. It will also reduce splashback onto leaves from contaminated soil. This will not only prevent damping off. It’s a good habit that will reduce the spread of other fungal diseases.


Opinions vary on whether damping off can be treated. There is no cure for damping off. Some gardeners have successfully sprinkled cinnamon over the soil around surviving seedlings that exhibit symptoms of damping off.

Nutrient deficiency

Browning leaf tips in true leaves can indicate a nutrient deficiency. The plant just isn’t getting what it needs to grow healthily. This may be due to no fault of your own. Seed starting mixes which we use to start seedlings, don’t offer a lot of nutrition.

Some aren’t even made of soil but rather a mixture of materials like moss and perlite. They provide a light, airy place for seeds to germinate and tiny seedling roots to grow, but once the seedlings produce true leaves and begin to photosynthesize, starting mixes cannot provide adequate nutrition.

Provide nutrients

You can make your own seed starting mix or add seed starting food to store-bought mixes. Seed starting fertilizer will feed seedlings until they are transplanted.


While seedlings with true leaves benefit from fertilizer, it is easy to overfeed. Too much fertilizer will cause the roots to burn and the seedling to turn brown and die.

Use fertilizers properly

Follow the directions on the fertilizer container. Use a fertilizer specifically for seedlings, and remember that they only need a little because they are so small.


While seeds require warmth to germinate and seedlings enjoy warmer temperatures, they can overheat quickly, causing leaves to start turning brown. This extra heat can come from using grow mats, grow lights, or being placed in an area with intense sunlight.

Reduce heat

Ensure that equipment is being used correctly. Turn off grow mats once seedlings emerge. The heat from grow lights placed too closely will burn seedlings. Provide ventilation and allow the seedling to enjoy a little shade from direct sunlight.


Too little water can cause seedlings to be brown from inadequate moisture.

Water regularly

Don’t let the soil stay dry for long periods. Water seedlings regularly, about every other day.


Too little water, as well as too much water, also causes seedlings to brown. In addition to turning brown, the differences are that underwatered leaves feel dry and crispy when touched. Overwatered leaves feel soft. You may even observe the leaves drooping downwards.

Water when appropriate

Do not water it if you observe that the soil is moist or wet around a particular seedling. A handy tool is a soil moisture meter. The meter is placed into the soil and measures the water content. It’s simple to use and read. 

Additional tips for proper seedling care

  • Check on plants daily – You’ll be able to spot any changes immediately.
  • Keep the temperature steady – A comfortable seedling is a happy seedling. Try to avoid fluctuating temperature changes where your seedlings are growing. 
  • Use the right size pot – While it might make sense to plant seedlings in large pots since they will get bigger, growing small seedlings in a large pot can have the opposite effect. It’s easy to overwater when using a large pot. The seedling cannot absorb all the water, and the water in larger pots takes longer to dry out. The seedling’s roots sit in water for prolonged periods and cause root rot.
  • Provide lots of light – Seedlings need bright light for several hours a day to thrive. If you don’t have a sunny spot most of the day, supplement by using grow lights.

Lastly, seedlings can be demanding. The type of care seedlings needs varies before and after germination. Providing proper care will help prevent many issues. Remember that seedlings will grow bigger, stronger, and become less dependent on us for their every need.

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