15 Common Problems With Garden Grown Pepper Plants

Are you running into some challenges with your garden grown pepper plants this season? Peppers are pretty low maintenance once they start to mature, but there are a few problems you may run into while trying to grow them. In this article, organic gardening expert Logan Hailey walks through the most common problems gardeners run into with pepper plants, and what to do about them.

A close up of red peppers growing in the garden that are wilted and dying. The focus is on the red fruits of the plant, with struggling foliage behind it.


Whether you prefer sweet or spicy, rainbow or red, peppers are an essential vegetable in the garden. Like their tomato and eggplant cousins, peppers love sunlight and heat. They’re also prone to similar problems like poor pollination rates, sunscald, and blossom end rot.

While it does require some patience, growing peppers is enjoyable and often very economical. These plants enjoy many of the same conditions as their tomato cousins. Nonetheless, it doesn’t always work out perfectly.

Your pepper patch can be bombarded by unexpected pests, diseases, nutrient problems, or temperature fluctuations that may have your plants looking a little strange. If you’re concerned about your spring pepper plants or disappointed by your summer yields, here are the most common problems gardeners face with pepper plants and how to overcome them!

Flowers, But No Fruit

Close-up of white small flowers of young peppers growing in the garden. White 6-7 petal flowers with yellow-green stamens. Bright green leaves with yellow tips grow on the stems of the plant. Slightly blurred background.
If your pepper plants have a lot of white flowers but no fruit, then there are pollination problems.

After waiting up to 70 days since seeding your peppers, it’s pretty frustrating when you haven’t seen a single fruit. Depending on the weather, pepper plants typically start producing flowers around the two-month mark. If you see a lot of white star-shaped flowers, but no developing fruit, you probably have a pollination issue.

Peppers are self-fertile, which means they don’t necessarily need cross-pollination like many other garden crops. You could hypothetically grow one plant alone and it would still set fruit. But the pollen still needs to reach the stigma (female part of the flower).

Pepper pollination is often a key problem with plants grown in a greenhouse or a protected area of the garden that doesn’t get much airflow. While they are often pollinated by the wind, bees can make each flower’s success far more likely.

How to Fix It

Hand pollination is far simpler than it sounds. You can manually stimulate the wind simply by shaking your plants around gently. You can also use a toothbrush or paintbrush to gently rub around the center bud of each flower.

For a longer-term solution, plant pollinator-attracting flowers like sweet alyssum, yarrow, and marigolds with your peppers.

No Flowers

Close-up of a pepper plant in the vegetable garden. Dense green foliage with several yellow leaves on the plant. The background is slightly blurred with green pepper plants.
Some reasons for lack of flowering can be extreme temperatures or lack of sunlight.

Flowers that haven’t pollinated yet are easily fixed, but if you have no flowers on your pepper plants at all, something must be off. Those little white flowers are what will eventually turn into your favorite bell peppers or hot peppers. Without them, you have no harvest at all.

First, check that you haven’t missed any developing flower buds near the centers of the plant. Next, check back in your planting calendar and see when you seeded or transplanted the plant. These long-season crops take up to 60 or even 90 days to start flowering depending on the variety.

If your pepper is well within the flowering range, the issue is probably temperature extremes or a lack of light. When it’s under 60°F, they may stop growing and refuse to send up any flowers.

These tender crops can’t handle prolonged cool temperatures. A period of warm weather followed by a sudden cold snap is especially confusing for the crop. This is most commonly a problem in the early season.

A lack of sunlight can also send these sun-loving plants into shock mode. The key symptoms of peppers with too much shade include no flowers and leggy, spindly growth.

How to Fix It

If your pepper plant was shocked by cold temperatures, the best thing you can do is wait it out for warm weather. The plant should resume making flower buds once it has enough heat.

Plant only once the danger of cold weather has passed. It’s helpful to create low tunnels for them by bending PVC pipes over the beds and covering them with row fabric or clear plastic. This will help buffer them from temperature extremes.

When your plants are getting too much shade, it could be time to prune away neighboring crops that are overshadowing them or transplant the whole plant. This is going to set back its growth, but it should be able to happily recover once it receives more sunshine.

In the future, remember to only plant peppers in areas with 6-8 hours of direct sunlight per day. Avoid tucking them beneath tall-growing crops like tomatoes or corn, which can cast big shadows in the afternoon.

Flowers Falling Off

Close-up of a man's palm holding a small white pepper flower. The white flower has 5 thin petals and green stamens in the center. The background is blurred with pepper plants growing in the garden.
Fallen flowers indicate that the plant is under stress due to extreme heat.

Surprisingly, a heat wave can cause their flowers to drop or stop developing. In spite of their summer-loving nature, extreme temperatures above 80°F or 90°F stress out pepper plants. This is more common in peak summer. You will likely see fallen flowers around the base of the plant.

Keep in mind that a little bit of flower drop is normal for peppers. They naturally produce more flowers than needed, so you’ll occasionally see a flower fall off here and there. But when large amounts of flowers are dead at the base or you don’t have any flowers on the plant at all, it’s time to take action.

How to Fix It

There is little you can do about extreme heat waves except try to nourish the plant with proper watering. Ensure your peppers aren’t under drought stress or being overwatered. Check the soil daily during hot weather and keep it consistently moist without being soggy. You may have to wait until the heat subsides for the plants to send out more blossoms.

Small Peppers

Closeup of a Red Bird's Eye chili or Thai chili with thick green leaves. A man's hand is holding a red chili pepper, about to pick it. Many long green and red pepper fruits grow on this plant.
The reasons for small peppers can be poor soil, lack of phosphorus, or an excess of nitrogen.

Tiny peppers could mean your plants just aren’t quite ready to be harvested. However, if the fruits don’t seem to be enlarging after a few weeks, you either have a fertility issue, an overcrowding problem, or you choose a small variety.

Peppers are moderate to heavy feeding crops that need plenty of fertility in the soil. Typically, a slow-release organic nitrogen source is best for the time of planting because it encourages quick establishment without causing an overgrowth of foliage. Once the plants start flowering, they need more phosphorus and less nitrogen to develop large fruits. 

Similarly, peppers planted too close together will inevitably yield small fruits. They need at least 12-18” between each plant, depending on the variety. Overcrowded plants will compete for water and nutrients, which means less energy to put into fruit production.

Lastly, you may have just planted a variety that doesn’t grow very large. For example, Japanese shishito peppers only mature to 4-5 inches in length. Jalapenos typically max out 3-5 inches. Check your seed packets to be sure you didn’t choose a dwarf or mini variety.

How to Fix It

If your plants are overcrowded, you may want to thin out every other plant to give them more space. Alternatively, you could try to carefully transplant them.

They need plenty of phosphorus to fuel fruit production. Bone meal, manure-based compost, and fish bone fertilizers are great for peppers. You can begin feeding the plant these P-rich sources around the time of flowering. Side dress based on the package instructions.

If you accidentally over-fertilize with nitrogen, you may want to add a teaspoon of epsom salts or prune away some of the extra foliage growth. Both actions should encourage the plant to  focus on growing large fruits rather than leaves.

Next season, choose larger-fruit varieties like ‘Corno di Toros’ (rainbow Italian peppers), ‘Big Jim’ (a grande´ chili pepper), or ‘Big Bertha’ (a sweet pepper). 

Deformed Fruit

Close-up of a pepper ripening on a bush in a garden bed. Deformed green pepper with a red barrel. The background is slightly blurred with pepper bushes growing in the garden.
Deformed fruits occur due to insufficient pollination of flowers or due to low night temperatures.

Misshapen or lopsided peppers are perfectly fine to eat, but not nearly as pretty as the ones in stores. If your plants are otherwise healthy and strong, the flowers may not have been fully pollinated or the plants were exposed to extended cold nighttime temperatures below 60°F.

How to Fix It

Like the flowering issues described above, you will need to remedy the situation with hand pollination, insectary plantings, and/or row cover to protect the plants from cold nights.

Young Plants Die From the Base

Close-up of a young pepper seedling planted in soil in a garden. The green leaves of the seedling are covered with a white bloom. The bottom leaf is yellowed due to disease.
This disease of seedlings develops in compacted, waterlogged soil.

A plant that gets cut off at the base has no chance of revitalizing itself. It can feel a bit like a pepper massacre when you discover several plants in a row have been “beheaded” right at the soil level.

Damping off is a seedling disease caused by a fungus-like organism that loves compacted, waterlogged soil and stagnant conditions. It causes the bottom portion of a baby pepper stem to turn white or brown and wither away to a floss-like thickness.

The plants quickly collapse and die from a lack of access to their root zone. Thankfully, it only attacks seedlings and doesn’t do much to juvenile or adult plants.

Cutworms are among the most damaging to pepper plants because they attack young plants right after transplanting. These fat grubs crawl up from the soil, curl around the base of the plant, and sever it right at ground level. A single cutworm can decapitate the stems of lots of young plants in just a single night. 

How to Fix It

The most important step for preventing damping off is improving the drainage of your soil mix. Whether you’re direct seeding or starting peppers indoors, the soil needs to allow water to quickly pass through it without getting soggy or waterlogged.

Compaction in the garden due to excess tillage or a lack of organic matter can cause similar issues. The quickest fix is simply amending with generous amounts of compost, perlite or vermiculite.

If you’re dealing with damping off regularly in your home nursery, you may want to invest in some fans and increase your spacing between plants. A lack of circulation is the second key cause of this disease. Prevent future seedling losses by simply improving airflow around the baby plants.

Dealing with cutworms is a bit more challenging. These moth larvae hide in the soil during daylight and come out to feed on plants at night. They look like gray, green, or silvery fat grubs in a “C” shape. They loop around the base of the plant and eat it away.

Getting Rid of Cutworms Naturally
  • At night, remove by hand and drop them in soapy water.
  • Apply diatomaceous earth or dried egg shells around the base of your plants.
  • Clear plant residue or mulch from the base of peppers.
  • Try stem protectors like nails, toothpicks, or drinking straws to straddle the stem base.
  • Attract chickens or birds to the garden to feast on the grubs.

Light-Colored, Dry, Sunburnt Fruits

Close-up of three peppers hanging from a stalk. Peppers are medium in size, green on one side and white on the other. The white side of the pepper is sunburn. A gray beetle sits on one of the peppers. The background is blurred pepper bushes growing in the garden.
Peppers can get sunburned due to excessive sun exposure to the fruit.

You may be surprised to know that peppers can get sunburnt, just like tomatoes. When exposed to too much light and heat, the leaves or developing fruits may have thin, pale, or dry areas on their skin. They may even turn black. Sunscald is especially problematic when a pepper plant has lost a lot of foliage to a disease or over-pruning.

How to Fix It

Peppers need a fair amount of leafy canopy over the fruits to protect them from direct sunlight. Ensure that your plants have vigorous foliage development by supplying a slow-release all-purpose fertilizer at the time of planting. You also want to be sure that you don’t remove too many leaves.

Check your plants for diseases and take appropriate action to prevent them so there are enough leaves to keep the fruits protected. Worst case scenario, you can use a shade cloth or floating row cover to protect the plants from the intense summer sun.

Black, Soft Spots on the Bottom

Close-up of a green pepper affected by tip rot. Green pepper with red bottom. The red bottom of the pepper is damaged by brown rot. Dark green dense foliage around the pepper.
Blossom end rot appears due to the wrong mineral balance of the soil.

Black, rotten spots at the base of your peppers are an obvious sign of blossom end rot. This issue is not technically a disease, but rather a cultural problem. Improper soil mineral balance (particularly with low calcium) or water stress are the likely culprits.

Peppers that are exposed to a lot of water at once and then long periods of dryness are more prone to blossom end rot. This stresses out the root system and fruits because they don’t have a reliable source of moisture, resulting in poor fruit development and rotting.

A lack of calcium availability can also lead to a breakdown in the fruit cell wall tissues, causing unsightly black or brown sunken spots at the base of peppers.

How to Fix It

You will have to remove plants that have already succumbed to rot. If the tops are still good quality, they are still perfectly edible once you cut off the base.

Next, you’ll want to adjust your watering schedule. Instead of causing big fluctuations in irrigation, try to maintain a consistent amount of moisture. Water using drip lines or soaker hoses at least 1-2 times per week in peak summer. Regularly check the soil moisture and never let the plants get soggy nor dry and wilted.

To improve calcium levels, add a handful of crushed eggshells, oyster shells, or a liquid crab and lobster shell fertilizer to each plant. You may also need to adjust your soil pH for optimum calcium availability.

A pH between 6.5 and 7.0 is ideal for calcium absorption. In acidic soils, you can add dolomitic lime, gypsum, or baking soda to raise the pH. In overly alkaline soils, add elemental sulfur, compost, or pine needles to lower the pH.

Stunted Growth With Leaf Spots

Close-up male hand holding a pair of infected pepper leaves. The leaves are infected with mosaic virus and have yellow-green mosaic patterns. A diseased plant is surrounded by the leaves of a healthy pepper plant.
The mosaic virus is transmitted by aphids, so the problem must be solved by getting rid of these parasites in the garden.

There are lots of potential causes for stunted growth, but when combined with these other symptoms, you’ve likely got a viral issue on your hands. Mosaic virus can attack peppers, tomatoes, tobacco, and other members of the nightshade family.

Symptoms of mosaic virus:

  • Leather-textured leaves.
  • Curled or wrinkled leaves.
  • Specks or ring-shaped spots.
  • Mosaic pattern of alternating dark and light spots on leaves or fruit.

How to Fix It

Remove infected plants immediately. Next, deal with any pest infestations. Mosaic virus is predominantly transmitted by aphids. A hard blast of water and a diluted neem oil spray are safe and fast fixes to an aphid problem.

You can also choose resistant varieties like ‘Gourmet’, ‘Ninja’, or ‘Islander’ bell peppers. Lastly, sanitize your hands and garden tools to prevent the further spread of mosaic virus. If you use tobacco, avoid doing it near your garden and never touch your plants after smoking.

Yellowing Leaves

Close-up of yellow leaves of a chili tree. Diseased yellow leaves alternate with healthy dark green leaves. Some leaves have yellow and brown spots. Two white pepper flowers bloom on a branch.
If their leaves start to turn yellow, then you need to add universal fertilizer and adjust the watering.

Yellow leaves are a fairly generic sign that your plants are unhappy. They may appear yellow  In peppers, it’s most commonly linked to a lack of fertility or overwatering. It could also indicate poor watering techniques as well.

How to Fix It

Provide peppers with a nice scoop of all-purpose fertilizer at the time of planting. You can also give them a bi-weekly dose of liquid fish and kelp fertilizer up until they start flowering.

If the soil is soggy or waterlogged, cut back on watering and add a compost mulch on the surface to improve drainage. Avoid overhead watering or timer water systems that may drown your plants. In the future, use a broadfork and compost to loosen the soil before planting.

Yellow or Brown Spots on Leaves

Close-up of a pepper bush with dense damaged foliage and ripe green fruits. Some leaves have a yellowish tint and small brown dots. One of the pepper fruits has black-brown decay.
Bacterial leaf spot is one of the common diseases that is difficult to get rid of.

Bacterial leaf spot is a common disease in pepper plants that causes leaves to die and fall. It is particularly destructive in the eastern United States under humid, warm summer conditions. The main symptoms are:

  • Water-soaked lesions on leaves.
  • Greenish-yellow to dark brown spots up to ¼ inch in diameter.
  • Dried tattered portions of leaves.
  • Raised scabs on the fruit.

How to Fix It

There are no known cures for plants that are already infected. You should remove them right away to prevent the disease from spreading. It’s important to keep old crop debris cleared from the garden because this is where the pathogen can overwinter.

Always source reputable disease-free seeds and transplants. You can also choose varieties that are resistant to bacterial leaf spot, including ‘King Arthur’ bell peppers, ‘Olympus’ bell peppers, and ‘Black Magic’ jalapenos.

Leaves Shrivel and Fall Off

A close-up of a pepper leaf on which sit many small translucent beetles called aphids and a couple of small flying whiteflies. This pale green leaf is held by a man's hand.
Whiteflies suck the juice from the leaves of the plant, after which the leaves begin to fade, turn yellow, and wrinkle.

Whiteflies are small winged insects that look a lot like aphids. They are sap-sucking white pests that leave behind a sugary honeydew residue that can lead to mold on the leaf surface. When whiteflies get out of hand, pepper leaves start to wilt, turn yellow or pale-colored, then shrivel and fall from the plant. Older plants are the most susceptible.

How to Fix It

Many whitefly species are resistant to chemical pesticides, so you’ll likely have to treat them with a homemade or organic spray. A 2:5 dilution of rubbing alcohol to water, plus a tablespoon of soap can be applied directly to the leaf surface (upper and undersides) in the evening.

You can also try neem solution or insecticidal soap. Avoid over-fertilizing because it promotes excessive foliage growth that attracts both whiteflies and aphids.

Large Amounts of Foliage Loss

Close-up of a hornworm on a pepper leaf. The hornworm has a bright green body with black and white stripes and white and black dots. The background is very blurry.
Hornworms can cause serious damage to your plant as they feed on leaves.

Known for their aggressive appetite for tomato plants, hornworms can cause equal amounts of damage to the plants. These giant nasty green caterpillars have a spiky horn and a nearly inexhaustible hunger for leaves, fruits, and flowers. If you notice a huge amount of your plants have gone missing overnight, hornworms are the likely culprit.

How to Fix It

In small gardens, these pests are large enough to make handpicking the most efficient. You can brush against plants and hear the worms “hiss” at you to find their camouflaged bodies. They like to hang out on the stems and leaves they’re currently defoliating. Drown them in soapy water or cut them in half with a knife.

For larger infestations, Bt (Bacillus thuringiensis) is a great organic bio-insecticide that uses the power of bacteria to wipe out these hungry caterpillars. For long-term prevention, plant companion flowers near your peppers to attract hornworm predators like parasitic wasps.

Tunnels Through Their Skins

Close-up of a small brown corn borer larva sitting on a green bud. The body of this larva has dark brown and white spots. The background is green blurred.
If you notice brown holes in the fruit, like tunnels, then you most likely have a problem with a corn borer.

The European corn borer is most common in the Midwest and eastern United States. It is the larvae of a pest moth that lays its eggs on peppers, corn, beans, potatoes, tomatoes, and apples. You will notice brown holes burrowed through the top of and through the fruit, like tunnels. They can also cause the rotting from the inside out.

How to Fix It

Infested peppers can’t be saved and are usually too gross to eat. Thankfully, Trichogramma wasps are the best science-backed biocontrol secret for controlling these larvae.

They parasitize both the moth and the larvae to cut infestations down very quickly. You can order them from a biocontrol website or plant flowers that attract predatory wasps, such as yarrow, dill, caraway, and lemon balm.

Whole Plants Collapse

Close-up of a withered pepper bush with two green-yellow rotten fruits. Withered, twisted, brown-spotted green leaves hang from a pepper bush. The background is blurred with withered pepper bushes.
Verticillium wilt affects the entire plant and it dies.

It’s pretty alarming when an entire pepper plant suddenly wilts and collapses. Verticillium wilt is a soil-borne disease that can attack everything from maple trees to landscape shrubs. It favors cold air and moisture, particularly in the fall. This aggressive fungal disease attacks seemingly without warning. Symptoms include:

  • Yellowing and drooping of branches or whole plants.
  • Edges of leaves roll inward.
  • Isolated whole plants wilt and collapse (while their neighbors remain untouched).
  • Dry or brown foliage.

How to Fix It

There is no known cure for this fungal disease. It persists in the soil for up to 10 years and great care must be taken to prevent its spread. Immediately dig up infected plants and burn or throw away the foliage. Sanitize all tools and gloves.

You can try solarizing the soil with clear plastic over the bed for several hot days. Always remove dead plant debris from the garden in the winter so there is nowhere for the fungus to feed on.

Final Thoughts

Ultimately, peppers aren’t hard to grow as long as they have plenty of sunshine, fertile soil, and consistent water. Remember to properly space your plants, give them moderate amounts of fertilizer (but not too much), and use row fabric or shade cloth to protect them from temperature extremes. Although peppers take their time to fruit, your patience will hopefully pay off with an abundance of flavorful fruits!

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