The 10 most common problems faced by cannabis seedlings and how to fix them

By: Contributor Grow

The time when a cannabis grow is at its most vulnerable is in the first few weeks after the seeds have germinated. And this is because tender cannabis seedlings can suffer from overheating, lack of food, lethal fungi, excess irrigation… Yes, marijuana is a robust and vigorous plant that can withstand many setbacks, but to provide it with some of that vigour, you need a solid foundation: in other words, a healthy seedling stage that allows it to develop in the best way possible.

The cannabis seedling stage is the most sensitive moment in the growing process. It comes after the germination phase and before the vegetative and flowering stages. It is during this key period that the first true roots and fan leaves appear.

These shoots thrive in moderately warm and very humid conditions, but they don’t tolerate stress very well, so they need a lot of protection to become robust vegetative plants. Make sure you provide your seedlings with the right amount of TLC, and you’ll be ready to obtain abundant yields a few months later.

What’s the seedling phase?

The seedling phase is the second stage of growth of cannabis, and it covers the first 2 to 3 weeks after germination. It starts when you place a germinated seed in a growing medium, and the radicle gives way to a stem with two rounded leaves called cotyledons. These cotyledons contain nutrients, and their function is to enable the feeding of the newly germinated plant, so that it can perform photosynthesis while the first pair of true leaves grows, developing leaflets with serrated edges.

As the seedling develops in the growing medium, its root system expands below ground starting from the main root, which branches into secondary and tertiary roots. During its first 2 weeks of life, a cannabis seedling should significantly increase in height and size: by the end of this period, it should have developed 3 to 4 pairs of true leaves. As it enters the vegetative phase, this little plant will no longer be considered a seedling.

New release! - RS11 (Rainbow Sherbet #11)

Immerse yourself in the world of a true THC lovers strain… Being able to surpass 30% THC, RS11 (or Rainbow Sherbet #11) is a testimony to the magic of the earth and a reminder that there is an immensity of beauty and mystery waiting to be discovered, even in the smallest things.

What does a healthy seedling look like?

Rapid growth and a bright green colour are both indicative signs of a healthy seedling. The stem will initially be thin, but it should be able to stand upright: a robust stem denotes good cell structure and overall health. The leaves should be curving slightly upwards as they look for light and should display a lush green colour with no signs of discoloration, wilt, or damage.

Well-formed seedlings have uniform growth patterns with a balanced distribution of leaves, branches, and stems. This symmetrical structure ensures adequate exposure to light and reduces the risk of competition between different parts of the plant, allowing the seedling to optimise the allocation of resources.

What types of problems can seedlings come across?

Unfortunately, many things can happen during those two weeks. In addition to possible issues related to pests or diseases, the most common problems that can affect seedlings are either excessive or insufficient irrigation, along with nutrient, temperature, and lighting issues. All of these are preventable setbacks that any experienced grower will be able to avoid effectively; but here are the most common causes and solutions in case you end up having to deal with any of them:

The seed shell is stuck to the cotyledons

Cause: You may not have planted the seed deep enough into the substrate for the shoot to get rid of the shell before it crosses to the surface. Or it could also be happening because the soil is too dry.

Solution: Spray the shell with water and remove it with your fingers. Avoid this problem by planting the seeds at a depth of three times their size; that is, plant a 5 mm seed at a depth of 1.5 – 2 cm. Ensure the soil remains constantly moist as the seed sprouts.

Lemon Haze Auto

If you are looking for an energizing and refreshing marijuana experience, Lemon Haze Auto is the perfect choice for you. With a high THC content (+18%), Lemon Haze Auto offers a very citric and refreshing taste. It is very easy to grow, making it suitable for beginners and experienced growers alike.

The seedling has a bent stem before it suddenly dies

Cause: If a healthy seedling has a bent stem, and then falls over and withers practically overnight, it is likely to be suffering from fungal wilting, a disease caused by fungi such as Pythium or Rhizoctonia. Moisture or nutrient excess can create conditions that promote this effect, which is known as ‘damping off’.

Solution: Although curing seedlings infected by these pathogens is not possible, they can certainly be prevented. Never reuse old substrate that might contain their spores. After planting your seeds, sprinkle sphagnum peat on the soil or growing medium to promote moisture absorption. Make sure you feed the seedlings with fertiliser but without overdoing it too much. You can also enrich the soil by adding beneficial microbes, such as mycorrhizal fungi.

The 10 most common problems faced by cannabis seedlings and how to fix them
Seedling affected by ‘damping-off’: you can say goodbye!

Long and thin stems, but tiny leaves

Cause: Seedlings need plenty of light as soon as they start growing. As artificial lamps are much less bright than the sun, seedlings try to stretch towards them when their tiny upper leaves are too far from them.

Solution: If you’re using fluorescent or LED lights, place them about 10 cm away from the top of the plants; and raise them further away as the plants grow higher. High-intensity lamps should be about 50 cm from the top of the plants: the fragile seedlings can get burnt if they are any closer.

Fallen leaves and stems

Cause: Overwatering the seedlings actually drowns them by depriving the roots of air, causing the leaves to droop down and the stems to begin to curve. Water excess is the common result of growing a small plant in a large pot, because the plant doesn’t absorb much moisture every day, so the soil in the container remains soaked.

Solution: Don’t plant seeds in potting soil, as this retains too much moisture. Instead, use a mix which includes peat or coco coir. Sow the seeds in a seedbed or small pots and get ready to transplant them to larger ones as they grow.

Seedlings lying down for no apparent reason

Cause: Wild cannabis plants develop strong stems as they dance softly with the breeze. This airflow is key to good structural integrity. However, extremely powerful ventilation can actually knock them down, causing bends in the stems that will prevent them from ever rising again.

Solution: Place an oscillating domestic fan near the seedlings, but select the lowest airflow, directing the jet towards the plant canopy. Staking the seedlings with a small stick and a string can also provide some extra grip to prevent them from being overcome by the airflow.

Purple Kush

Purple Kush is a popular strain of cannabis known for its deep purple color and potent sedative effects. Purple Kush is a strain that’s born to thrive. You’ll be able to enjoy dramatic flowering in 60 days, dazzling your garden with a festival of colours and aromas, while purple tones will begin to appear in swollen buds that are loaded with resin from the fourth week.

Curly and brittle leaves

Cause: Even a few hours without water can slow down the growth of seedlings; and, after a day, their leaves may begin to curve to try to retain moisture. Hot grow lights and dry air inside heated houses can also quickly dehydrate seedlings.

Solution: Plant them in a substrate mix that includes perlite or vermiculite, i.e. natural minerals that retain moisture and disperse it as needed. Keep the mixture slightly moist, but not soaked, so the plants don’t dry or drown.

The tips of the leaves turn yellow or brown, and the edges curve upwards

Cause: Warm temperatures (between 23 and 26ºC) are ideal for seed germination, but the delicate seedlings can overheat due to high-intensity lighting, lack of ventilation, or other reasons, which causes the foliage to start to burn at the edges.

Solution: Keep your indoor grow at 20 – 22ºC while the seedlings get established. Leave a fan gently blowing around to let in fresh air and prevent stagnant air from heating up.

The 10 most common problems faced by cannabis seedlings and how to fix them
Seedling suffering heat stress

Stagnant growth, or pale or yellow-striped leaves

Cause: Seeds contain all the nutrients that they need to germinate and develop their first pair of leaves, but after that they need to be provided with additional feeding, unless the substrate mix already includes it. When a seedling seems to have stopped growing for a few days and the leaves have turned pale or yellow, they need nitrogen, which is the essential nutrient for healthy green growth.

Solution: After the two embryonic leaves (cotyledons) appear, start feeding the seedlings with a nitrogen-rich seedling fertiliser. Follow the dilution recommendations: any nutrient excess that the seedling can’t absorb can become the perfect breeding ground for destructive fungi.

Purple leaves and stagnant growth

Cause: Phosphorus is another essential nutrient for the development of the roots. When it is scarce, the growth of the seedlings stops and the leaves can take on a slight dark green, almost bluish colour. The stems and petioles can also acquire that purple tone.

Solution: Once the leaves have appeared, start fertilising the plants with a nutrient formula rich in phosphorus. Check the pH of the nutrient solution to ensure that it is suitable for your growing system (soil or hydroponics): if the liquid is too acidic or alkaline, the seedlings won’t be able to absorb the phosphorus.

The 10 most common problems faced by cannabis seedlings and how to fix them
Seedling with nutrient deficiency or pH problems

Yellow spots or black mould on the first pairs of leaves

Cause: Whiteflies or substrate mosquitoes are common pests in indoor grows that can feed on weak seedlings. They suck the sap, leaving yellow spots behind. Worse still, when they suck more sap than they can digest, they excrete the excess in the form of a sticky substance (called ‘honeydew’) that they deposit on the leaves. This can lead to the emergence of saprophytic fungi such as black mould (or sooty mould), which can hinder photosynthesis.

Solution: The safest way to protect your seedlings is to use sticky traps that catch the flies before they can cause any damage. When the plants grow a little more, you can eliminate pests with insecticide soap, neem oil, or other biological remedies for pest control.


The seedling stage only lasts a couple of weeks, but what you get up to during that period will have a massive impact on the final product. Ideally, your seedlings should be kept in a warm and moist environment (20-25°C / 65-70% relative humidity), with good light and not too many nutrients. Keeping things simple at the start is the best way to go for your plants to reward you with an abundant yield later on. Happy growing!

Kannabia Seeds Company sells to its customers a product collection, a souvenir. We cannot and we shall not give growing advice since our product is not intended for this purpose.

Kannabia accept no responsibility for any illegal use made by third parties of information published. The cultivation of cannabis for personal consumption is an activity subject to legal restrictions that vary from state to state. We recommend consultation of the legislation in force in your country of residence to avoid participation in any illegal activity.

New, US Genetics


From: 139.00€