Why Does My Poblano Pepper Plant Have Brown Spots?

It’s always a huge bummer when brown spots start to appear on your poblano peppers. It’s vital to identify what kind of brown spots they are so you can get to the root of the problem and treat them ASAP!

Poblano pepper plants develop brown spots for various reasons. Some potential causes include calcium deficiencies, excessive sun, fungi, viruses, and more. Depending on the root cause, the appearance of the spots may differ and may manifest as bacterial leaf spots, blossom end rot, Anthracnose fruit rot, cucumber mosaic virus, and sunscald.

Keep reading to learn more about each of these causes, plus prevention and treatment!

Why are my poblano peppers getting brown spots?

There’s nothing more frustrating than getting excited over a growing fruit, only to discover brown spots on it.

To treat your peppers, you need to discover the cause of the brown spots. Your poblano peppers may be getting brown spots for many different reasons, including:

  • calcium deficiencies
  • excessive sun
  • fungi
  • viruses

It can feel like there are nearly endless reasons why poblano peppers may end up with brown spots. And to be fair, it’s barely an exaggeration! 

For example, calcium deficiencies can cause blossom end rot. On the other hand, overexposure to the sun can cause sunscald. Bacterial leaf spots can cause spots on their own and then lead to sun scald. It never ends!

This article will go point-by-point so you know how to identify, prevent, and treat different causes behind poblano pepper brown spots.

How do you treat brown spots on poblano pepper plants?

Treatment of brown spots really depends on the cause behind them.

To treat brown spots on poblano pepper plants, you first need to identify what is causing the brown spots. For example, fungicides can help treat Anthracnose fruit rot. Meanwhile, a little extra shade can treat sunscald. Going easy on nitrogen fertilization can help treat blossom end rot.

Reasons behind brown spots on poblano pepper plants include:

Treating brown spots on poblano pepper plants depends on which of the above reasons is causing your brown spots.

One thing that all treatments have in common is that prevention is the name of the game. For example, bacterial leaf spot prevention includes sanitizing seeds before planting. Meanwhile, blossom end rot prevention includes not overfertilizing. 

No matter what, always inspect your poblano transplants before bringing them home!

Bacterial leaf spot

Bacterial leaf spot is both the most common and destructive disease affecting poblano peppers in the eastern US. Different strains are specific to different cultivars.

Fruit yields can drastically decrease as leaves drop due to bacterial leaf spot, decreasing photosynthesis and therefore plant health.

In addition, the dropping of leaves can increase the likelihood of sunscald – a double whammy!

What does bacterial leaf spot look like?

Bacterial leaf spot can appear as leaf spots, fruit spots, and/or stem cankers. The earliest symptoms tend to be wet lesions on leaves that turn dark brown.

“Raised, scab-like spots” may show up on fruit. This does not directly cause the peppers to rot, but the lesion will make the fruit more susceptible to pathogens that will.

How do you treat pepper bacterial leaf spots?

To mitigate bacterial leaf spot, use pathogen-free seeds and disease-free transplants. Inspect your poblanos carefully before you take them home from the nursery.

To treat seeds, wash them in a 2:8 Clorox-to-water solution. You can also soak them for 30 minutes in hot water. That being said, bleach treatment is the better option because it won’t affect germination rates.

Another proactive step to take is using products that have beneficial microorganisms.

Rotate your crops each season to lower the likelihood of pathogen spread.

The best way to manage BLS is to combine multiple methods integratively to ensure happy and healthy poblano plants!

Blossom end rot

Blossom end rot takes place when peppers have a calcium deficiency. It breaks down the tissues of your fruit to create a mushy spot.

Agriculturally, blossom end rot can cause disastrous crop losses.

What does blossom end rot look like?

Blossom end rot starts off as a yellow sunken area on your poblano peppers. It expands and collapses until it eventually turns black thanks to fungus colonization.

Peppers affected with BER will often change color prematurely as if ripening faster.

How do you treat blossom end rot?

Control of BER starts with managing irrigation/water supply and nitrogen fertilizer. Poblano peppers require enough water during stress such as dry winds, droughts, and particularly sunny and hot weather.

It’s vital not to over-fertilize your peppers with nitrogen. Excessive nitrogen levels lead to excess vegetation, which can cause calcium deficiencies (leading to BER).

Adequately turn over the soil before planting so that there aren’t any shallow compaction zones that would impact roots.

Anthracnose fruit rot

Anthracnose is most present during hot, rainy spells. It can attack both mature and immature fruits.

Anthracnose is caused by a fungus within a group of common plant pathogens.

Widespread outbreaks have taken place on multiple pepper varieties ranging from bell to cubanelle to jalapeno. 

What does Anthracnose fruit rot look like?

Anthracnose can cause disease in all parts of your poblano pepper plant. 

Symptoms typically start to show themselves as “water-soaked lesions” that then become soft, indented, and tan. There are typically multiple lesions per fruit. The lesions evolve over time. They start to get covered with “gelatinous spores” from fungus. Concentric rings appear as well.

Lesions can be brown or orange to begin with and then evolve into a deep black.

How do you treat Anthracnose fruit rot?

As always, prevention is the best way to treat a disease. 

To begin, the seeds of infected plants should not be saved and planted again. If your peppers were infected by Anthracnose the previous year, you should rotate your crops for at least two years following. 

Transplants need to be kept tidy with extensive weeding. The garden needs good drainage with no infected plant debris lying around. Keeping insects off of your plants in order to prevent wounds is a helpful way to avoid an entrance point for the disease to infect your peppers.

If prevention doesn’t work, certain fungicides may be able to help mitigate damage.

Cucumber mosaic virus (CMV)

Cucumber mosaic virus is one of the most threatening pepper viruses around the world.

There are many strains, all of which can attack poblano pepper plants.

What does cucumber mosaic virus look like?

CMV causes ring spots that can appear on both the foliage and fruits. These spots are a reaction to the early infection of the virus. 

Your peppers may also start appearing unhealthy overall, or “dull.” Symptoms are worse if your plant is affected early on in its life.

How do you treat cucumber mosaic virus?

The best way to treat CMV is to avoid it altogether. It’s often spread by weeds or aphids onto your pepper plants, although insecticides can’t prevent it.

Mineral oil sprays are used in large operations in the south to avoid spread aphids.

Keep your peppers away from weedy border areas and grow them next to plants such as corn that can work as a “nonsusceptible barrier crop.”


Sunscald takes place when poblano peppers are overexposed to direct sunlight.

Typically, plants have enough foliage to protect the fruits from the sun. But plants with a lack of sufficient canopy or that were over-pruned are susceptible to being scalded.

Sunscald is even more likely if your peppers have another disease, such as bacterial leaf spot, that causes them to drop their leaves.

What does sun scald look like?

Sunscald looks like a tan burn on your peppers. 

How do you treat pepper sunscald?

Prevent sunscald by avoiding pruning directly above the fruit. 

If a plant doesn’t have enough foliage and keeps developing sunscald, move it somewhere where it will get more shade!