Why are my bell peppers turning black?

Most cannabis growers worry if we see purple stems, stalks, and petioles on our marijuana plants.

The color of leaves, stems, stalks, and petioles are a big part of our marijuana plant’s language as it tries to tell us if it’s happy or suffering.

Purple stems may be telling you that your plants will grow slower, buds will form slowly, buds will be smaller and less developed.

Purple stems, stalks, and petioles may be a warning sign of problems with nutrients, root zone pH, plant health, or grow room environment.

A stressed cannabis plant will often have purple stems and other parts.

But… some marijuana strains are genetically programmed to have purple stalks, stems, petioles, and leaves.

Check out these beautiful purple marijuana strains, for example.

You can discover if the strain you’re growing is genetically programmed to be purple by looking at strain descriptions, photos, and YouTube videos… and by asking the strain’s breeder.

If your grow op has multiple strains all fed and lit the same way but only one strain is going purple, and if the purple strain is growing as well as all the other strains, you’ve probably got nothing to worry about.

However if you’re growing multiple strains and most or all plants have purple stems, petioles, and stalks, you’ve likely got problems to diagnose and fix, especially if the strains aren’t known to be purple strains.

The most common purple problems come from hydroponics nutrients disorders and root zone issues.

Phosphorus and magnesium lockout or deficiencies are at the top of the list.

(Read here about nutrients lockout).

Purple stems can also come from nitrogen or potassium deficiencies or lockouts.

Nutrients issues can be frustratingly complicated.

Please look at this series of articles giving you a scientific way of diagnosing and fixing nutrients problems.

Fixing magnesium deficiencies is easier than fixing phosphorus, nitrogen, or potassium problems.

You root or foliar feed Epsom salts at a rate of ¼ teaspoon of Epsom salts per gallon root feed or a 130 ppm foliar feed at 5.7 pH.

You can root feed Sensi Cal-Mag in grow phase and the first three weeks of bloom phase.

In bloom phase, root feed Bud Candy, Bud Factor X, and Microbial Munch (all three have magnesium).

Fixing phosphorus deficiency is challenging because there are few solo phosphorus supplements.

If I suspect phosphorus deficiency, I add B-52 in grow phase, and B-52 and Big Bud in bloom phase.

The B-52 provides added phosphorus, nitrogen, and potassium, along with B vitamins that help stressed plants.

B-vitamins also increase bud development.

Beware that most bloom boosters contain way too much phosphorus in relation to potassium.

Inferior hydroponics base nutrients and supplements can create lockout and deficiencies, as can incorrect root zone pH, bad water, overwatering, and overfeeding.

And if you routinely add a solo element like magnesium into your root zone, you may eventually create other problems, such as nutrients lockout.

Only feed materials such as Epsom salts for one or two watering cycles, then stop using that material, and see what happens.

If you’ve tried flushing, adding individual nutrient elements such as magnesium, eliminating grow room environmental problems, pests, and diseases, and you still have purple stems, petioles and other plant parts, watch your purpling plants closely.

If they’re purple but they’re otherwise growing well, no worries.

But if they’re growing slowly or not at all, if bud development is delayed and inadequate, if they’re not using much water or nutrients, this is most likely a sign of a defective strain.

This is especially verified if you’re growing other strains in the exact same environment and they’re doing great.

For example, I had a 3000-watt grow room with five different strains.

Four strains grew fine and yielded big.

One strain had purple stems starting three weeks into grow phase.

I couldn’t fix it.

Those plants grew slowly with weak stems and stalks.

They didn’t yield enough weight, even though the buds were potent.

I won’t grow that strain again!

The Stems Of My Marijuana Plants Are Purple!

Purple-stemmed marijuana plants can be a bit scary, especially if you‘ve never seen such a sight before. However, rest assured, it probably just looks a lot worse than it really is and is easily remedied.

Why purple?

If you are an indoor grower, your plant is relatively young with leaves of average size, and the purple stems emanate from the top then that purpling is related to genetics.

Some marijuana strains naturally grow purple stems which cause their budding seedlings to appear even more purplish in cooler temps at night.

Other strains, especially those that show stems of seedlings that have turned purple, and have no other issues, have been genetically modified to do so. You will notice over time that purpling will come and go depending on climate and other factors.

A solution for purple stems

Although you may feel worried when seeing purple stems on your marijuana plants for the first time, it’s important not to rush into any changes for the first 1-2 weeks after discovering them.

This is particularly important if the plant and its leaves both appear to be otherwise healthy. In many cases, waiting for this period will give the plant ample time to return to its lively green color, if it’s capable.

If your plant is experiencing slowed growth, on the other hand, or if its leaves are fading, your plant might have a magnesium deficiency. This nutrient deficiency is one of the most common non-genetic reasons for purple stems.

If this is the culprit, fortunately, it is easily treatable. To ensure your plant has the minerals it needs, simply add magnesium in your next watering by carrying out one of these strategies:

  • Use Epsom Salt, by adding one tablespoon per gallon of water.
  • Use Cal-Mag per package instructions.
  • Use a nutrient system that provides time-released magnesium for your plant.

If you think the purple stems on your plant can be attributed to a magnesium deficiency, make sure to read our other article about how to best identify magnesium deficiency.

Thanks for reading. Please leave comments or questions below and don’t forget to download my free grow bible.


Should I be concerned about these purple stems and dead leaves?

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Discolored Pepper Stems: What Causes Black Joints On Pepper Plants

Peppers are probably one of the most commonly grown vegetable in the home garden. They’re easy to grow, easy to care for, and are seldom affected by pepper plant problems. However, many people do have issues on occasion with discolored pepper stems or with pepper plants turning black.

Why Pepper Plants Have Black Streaks on Stem

Growing peppers in your garden can be a rewarding and nourishing experience. Peppers are usually easy to grow, generate a lot of fruit and are not bothered by many pests. One commonly reported concern with regards to peppers, however, has to do with a purple-black coloration that occurs on the stems.

For some peppers, purple or black stems are normal and as long as the plant looks healthy, you shouldn’t worry about the dark coloration on the stem. While some peppers, such as bell peppers, commonly have purple or black stems that are completely normal, there are some diseases that do cause discolored pepper stems. Proper diagnosis and treatment of disease will help keep your entire crop of peppers from going to waste.

Discolored Pepper Stems

If your pepper plant has a dark black ring that encircles the stem, it may have a disease known as phytophthora blight. Besides your pepper plants turning black, you’ll notice your plant wilting and suddenly turning yellow. This is due to the fact that no nutrients or water can pass up through the ring that’s girdling the stem.

To avoid this disease along with many other pepper plant problems, don’t plant peppers in soil where eggplant, gourds or tomatoes have been planted in the past three years. Avoid overwatering and watering from overhead.

Black Joints on Pepper Plant

Got black joints on pepper plant? Black joints on your plant may actually be black cankers caused by fusarium, which is a fungal disease. This disease causes fruit to turn black and mushy.

It’s imperative to prune diseased plant parts to keep the fungal infection from spreading to other parts of the plant. Keep pruning tools sterilized and avoid watering plants from overhead. Overcrowding sometimes causes this problem as well.

So next time you notice your pepper plants turning black and want to know why pepper plants have black streaks on stem parts, be sure to give them a closer look. While bell peppers naturally have discolored pepper stems, black rings accompanied by wilting or yellowing and cankers or soft spots on the stem are indications of something more serious.

Why are my Chillies Black?

Around this time every year I always get a handful of emails from readers asking me about black chillies. Why are my chillies black? What have I done wrong? Can I eat black chillies? Are my chilli plants mutant?!

As part of the natural ripening process it is quite common for chilli peppers to be black in appearance or have black/dark streaks on them.

Most chillies such as the common Birds Eye or Cayenne will start off life green and ripen through to orange or red. However as the pods start to ripen, the sugar content in the fruit increases and the skin will often turn a dark brown or black colour temporarily.

As the ripening process continues the blackness will eventually give way to red. These changes in colour can seem like they are taking an age to happen, especially when you’re waiting for pods to ripen at the start of the summer!

How long this ripening process takes depends on a number of different factors such as weather, feeding regime and watering levels. There are no hard or fast rules how long the ripening process takes and the only thing that tends to speed up the process is the amount of sun your plants are getting.

Usually however these changes happen so slowly that you begin to think there is something wrong with your plants. Then inevitably you’ll turn away for a second and your plant will suddenly be full of wonderfully ripe red pods.

The lesson here is to be patient!

Of course there are some varieties of chilli that naturally are black or brown in colour when ripe. The most popular such variety is the Chocolate Habanero (pictured below, these are great for making chutney by the way) that ripens from green through to a deep chocolatey brown colour.

Chillies can be eaten at any stage in the ripening process, including when they are black or brown in appearance. However the flavours can change significantly throughout. The best way to work out what is best for your tastes is to try some pods at different stages of ripeness!

Jalapeños are the perfect addition to any meal thanks to their spicy heat flavor. While most jalapeños are green when you pick them, some can be black or starting to turn black. If you’ve noticed this, you may be wondering how to stop jalapeños from turning black. However, you should understand what causes jalapeños to turn black in the first place.

Step One: Recognize what shade of green your jalapeno should be

A Jalapeño should be either a forest green, light green or medium green. If it’s black or is turning black, there are several possible causes. The pepper will naturally turn black during the ripening process. Another possible cause is something called black rot. This can occur if the plants have had excessive watering. It should be easy to see the difference between a normal pepper with black coloring and one that has signs of rot.

Step Two: Pick your jalapeño before it is fully ripe

Typically, a jalapeño ripens in a week, although the timing can vary. That’s why it’s best to pick your pepper before it has the chance to turn black. To determine if your pepper is ripe, you must check it frequently. On average, the jalapeño is anywhere from 5 to 10 centimeters when it’s ripe and has a coloring that is deep green and glossy.

Step Three: Enjoy your green jalapeño

If you follow through with the steps listed above, you will end up with a jalapeño pepper that is green and tasty.

Keep in Mind:

While you don’t want to end up with a black jalapeño pepper, this doesn’t necessarily spell out trouble for you. There’s actually nothing wrong with black peppers, unless they are rotten. In that case, you obviously wouldn’t want to eat them.

Usually, black peppers are much hotter than green ones, so if you prefer a spicier taste you may want to opt for a pepper that is black. Knowing the perfect time to pick jalapeño peppers can be challenging. Jalapeño peppers that are black usually mean that the vegetable is ripe. If you end up picking your pepper too soon to avoid it turning black, you may have a pepper that isn’t ripe enough. Ripe peppers taste differently from ones that aren’t ripe, but the difference is not big enough for most people to notice. You should always strive for a green jalapeño pepper that is just the right ripeness.

Blossom-End Rot in Bell Pepper: Causes and Prevention1

George J. Hochmuth and Robert C. Hochmuth2

Figure 7.

Young pepper crop on black-plastic mulched beds with drip irrigation at the North Florida Research and Education Center-Suwannee Valley, in Live Oak, Florida.


Bell pepper is a major vegetable crop in Florida, grown on nearly 20,000 acres with a total value of nearly $200 million. Pepper is subject to many biotic diseases, caused by fungi, bacteria, and viruses, and to several abiotic or physiological disorders, such as nutrient deficiencies. One of the most commonly observed disorders of pepper is blossom-end rot (BER) which can cause major crop loss. This fact sheet describes BER, its causes, and prevention.


Calcium (Ca) is a required element for plants to grow normally and complete their life cycle, producing fruits and seeds. Calcium ions are present in the soil solution in which the pepper roots are growing. Blossom-end rot results from a calcium (Ca) deficiency in young, rapidly expanding pepper fruit tissues.

Blossom-end rot symptoms begin as a light green or yellow-colored sunken spot and expand to a larger collapsed area that begins to turn black from colonization typically by saprophytic Alternaria fungal species. BER-affected fruits tend to turn color prematurely from green to brown and then red (or yellow if yellow is the mature color of the variety in question). Large BER spots can be subject to infection from soft-rot bacteria.

Figure 1.

Early tissue breakdown and symptoms of BER.

Credit: Bob Hochmuth
Figure 2.

Advanced BER of pepper fruits in the field. Saprophytic Alternaria spp. grow on the BER lesions causing the black coloration.

Credit: Bob Hochmuth
Figure 3.

Advanced BER symptoms on pepper fruits on the plant showing premature coloration.

Credit: Bob Hochmuth
Figure 4.

Advanced BER accompanied by secondary bacterial soft rot (shiny areas at the margins of the BER lesions).

Credit: Bob Hochmuth

Calcium Physiology

To understand blossom-end rot causes and control, we need to understand some basic information about Ca uptake from the soil and its transport and function in the plant. Calcium deficiency in the fruits results from two types of problems in Ca delivery to the plant. First, there could be an inadequate concentration of Ca in the soil solution. Second, there could be inadequate concentrations or amounts of Ca being delivered to the rapidly growing tissues, such as leaves or fruits. Calcium undergoes various reactions in the soil such that Ca is removed from the soil solution by precipitation or added to the solution as the Ca minerals in the soil or calcium fertilizer dissolves. Soils under regular vegetable production usually contain enough Ca for normal crop growth; typically other factors, explained below, lead to BER.

Plant root morphology plays an important role in Ca nutrition of the plant. Nearly all of the Ca is taken up by the plant by the young root tips, perhaps most in the newest one inch of the root tip. In older portions of the root, the cells in the endodermal layer are surrounded by a layer of suberin on their radial and transverse walls, called the Casparian strip (Figure 5). Calcium in the soil solution is taken into the pepper root tips by a passive uptake process. Passive uptake means the plant expends no energy to take Ca into the plant. The Ca ion does not pass actively across a cell membrane as phosphorus, nitrogen, and potassium do but rather moves in the water solution in the intercellular spaces between root cells and then across the root, following the flow of water, and then into the xylem vessel. The Casparian strip, in the older portions of the root, prevents the lateral, passive movement of water and ions toward the xylem. The xylem vessel is the water conducting tissue (“tubes”) that moves water containing Ca ions to the top of the plant.

Figure 5.

Cross section of a root showing the Casparian strip and symplastic (active) and apoplastic (passive) ion uptake across the root. Ca uptake is most effective in younger root tips, where the Casparian strip is not fully developed.

Credit: Greg Means and George Hochmuth

Calcium ions mostly move with the water in the transpiration stream, up the xylem vessel, toward the upper plant parts. Water is moved up the stem as water is lost (transpired) from leaves. Transpiration is the process by which plants lose water from plant organs such as leaves and fruits. Water is lost from the surface of leaves through special openings called stomata. More water from the xylem stream replaces water that is transpired. Transpiration is the main pathway by which Ca ions reach young growing leaves, stems, and fruits. Another mechanism for Ca to reach the tops of plants is by “root pressure” where roots, water, and Ca ions are forced up the xylem under conditions of low transpiration, such as during the night, when relative humidity is high. Growers should make sure there is ample soil moisture at night, since root pressure can serve as a major mechanism to get Ca ions into fruits.

Calcium is required in cell wall development in actively dividing and expanding cells. Calcium also is required in calcium pectate which is part of the middle lamella that “glues” cells together forming tissues (Figure 6). Under Ca deficiency, cells and tissues collapse, leak cell fluids, and die. This death of cells and tissues leads to the typical collapsed and sunken areas on the tip, or the blossom-end area of young, rapidly growing fruits.

In most BER cases in Florida, it is the relationship between Ca movement in the plant and transpiration in leaves that is most likely the basis for Ca deficiency in fruits. Calcium moves with the transpiration stream, therefore, most Ca will be transported to those organs with the greatest transpiration rate. The organs with the greatest transpiration rate are large, rapidly expanding leaves because these organs have the greatest concentration of fully developed stomata. In addition, there is a less developed waxy cuticle covering the epidermal cells at the surface of the leaf, compared to older leaves. The cuticle reduces water evaporation from the surface of the leaf.

Rapidly growing pepper fruits do not transpire as much as leaves do, and fruits have a waxy covering that prevents water loss. Low transpiration and evaporation rates in the fruits means less Ca transported to the fruits. These characteristics place fruits at a distinct disadvantage in competing for Ca ions as they are transported in the plant. Any plant growth and developmental factors that tip the balance of Ca transport in favor of leaves will predispose fruits to Ca deficiency, potentially leading the BER. BER is typically most prevalent on the earliest fruits on the plant (“crown fruits”), because there is the greatest ratio of leaf surface area to fruit surface area at this growth stage. Although early fruits are most vulnerable to Ca starvation compared to fruits that set later in the growth cycle of the plant, periodic BER can be manifest at any time given certain situations described below.

Figure 6.

Neighboring cells depicting Ca distribution.

Credit: Greg Means and George Hochmuth

Calcium Deficiency

Calcium in the soil solution comes from several native mineral sources in the soil, such as calcium carbonate (limestone), apatite (calcium phosphate), and gypsum (calcium sulfate). These minerals are sometimes added as fertilizer. Growers also can supply Ca fertilizer sources such as calcium nitrate, calcium chloride, or various chelated calcium fertilizer materials. These fertilizers are often applied through a drip irrigation system to supply Ca to the root zone. Some soils should not require Ca fertilization. For example, soils with large amounts of calcium carbonate are likely to have ample Ca ions in the soil solution. This situation would occur where soils contain marine shells or are coral soils such as those used for vegetable production in the Homestead, Florida area.

Another source of Ca ions is the well water used for irrigation. In Florida, well water comes from the Floridan aquifer which is located in the limestone rock underlying most of Florida. Water pumped from this aquifer will contain significant concentrations of Ca, often on the order of 100 parts per million. This concentration is similar to concentrations of Ca in many recommended hydroponic nutrient solutions. Low-Ca irrigation water would be rare in peninsular Florida.

Inadequate Ca in the soil solution can be confirmed with a soil test, such as the Mehlich-1 soil test. A Mehlich-1 soil test index of 300 parts per million or greater indicates adequate concentrations of Ca in the soil. General knowledge about the soil chemistry in the field also can help predict Ca availability levels for the crop.

Factors Predisposing Fruits to BER

There are plant factors that can increase the likelihood of BER. Growing conditions that increase leaf and shoot growth could lead to a priority movement of Ca toward leaves. Excessive nitrogen fertilization leads to rapid shoot growth. If rapid shoot growth is occurring simultaneous with fruit set and growth, then BER could result, because Ca is preferentially moved to the growing leaves as opposed to the fruits.

Excess fertilization also can increase the soluble salt concentration in the soil. High soluble salt concentrations in the soil solution near the roots can lead to a diffusion gradient that favors movement of water from a low salt concentration environment (the root) to the high salt environment (the soil solution). This condition makes it more difficult for the root to take up water (and Ca).

Inadequate irrigation could predispose the fruits to Ca deficiency. Water stress leads to a general reduction in Ca transported in the plant. Since fruits are the least likely to receive ample Ca delivery under the best of conditions, then it follows that expanding fruits will be starved for Ca under water stress. Inadequate water delivery to the plant could result from several causes. A poorly managed irrigation system, resulting in inadequate water delivery to the plant, is a common underlying cause. Root pruning from mechanical cultivation, diseases, nematodes, or flooding also could reduce water uptake.

Prevention of BER

Minimizing the likelihood of BER takes a concentrated effort to reduce the conditions that predispose the pepper crop to BER. An understanding of Ca physiology in the plant and why BER might occur is needed before embarking on a management program. For example, knowing that Ca moves in the water stream in the plant, the grower might opt for increasing the level of irrigation instead of applying more Ca fertilizer.

  • Control of BER begins with irrigation and nitrogen fertilizer management. The irrigation system must be designed to be able to supply adequate water especially during those high stress periods of the growing season. Greatest stress occurs during prolonged droughts and when dry winds blow for extended periods. Technologies and equipment that can monitor soil moisture should be employed by growers. Growers should strive for uniform soil moisture during the day and night. This might mean more irrigation during the hotter times of the day, especially during the fruit-set phase of crop development.

  • Nitrogen fertilizers should not be applied in excessive amounts. High nitrogen rates, whether from chemical fertilizers or excessive manure applications, will lead to proliferation of leaves and branches. Plants with excessive vegetative growth will be most likely to suffer from Ca deficiency in the fruits.

  • Growers should have knowledge of their soil and irrigation water Ca concentrations. If these sources are supplying adequate amounts of Ca, then the grower would not need to supplement the soil Ca with Ca fertilizers. Calcium fertilizer materials, especially for soluble fertilizers, are typically expensive.

  • Foliarly-applied Ca fertilizers are not likely to correct or prevent BER. Ca ions in ample amounts are not actively mobilized from the leaf downward to the fruits.

  • Pepper plants need a well prepared soil with no shallow compaction zones that would restrict root growth. Restricted root growth could lessen that plant’s ability to find water under dry soil conditions. Control of any factors that can damage roots is important for controlling BER. Root diseases, nematodes, and flooding should be controlled.

  • Using polyethylene mulches, black under cool spring seasons and silver or white-on-black in the summer or fall seasons will moderate the soil temperature leading to more optimum root function and water uptake, which leads to improved Ca uptake.

  • Sometimes multiple factors contribute to the development of BER. For example, a crop that is highly vegetative from excessive nitrogen would be more likely to suffer from water stress under dry weather conditions or inadequate irrigation. Although the irrigation program might be adequate early in the plant growth cycle, there could be short-term water stress and BER as the plants reach full size and are setting and enlarging fruits.


Blossom-end rot is not always a straightforward fruit disorder, in either cause or prevention. Growers should understand Ca nutrition and physiology in the soil and pepper plant. This knowledge is the key to preventing the conditions that predispose pepper crops to BER. Two of the major factors, under grower control, that minimize the chances for BER, are proper nitrogen fertilization and optimum irrigation management.



This document is SL 284, one of a series of the Soil and Water Science Department, UF/IFAS Extension. Original publication date March 2009. Reviewed March 2015. Visit the EDIS website at http://edis.ifas.ufl.edu.

George J. Hochmuth, professor, Department of Soil and Water Science; and Robert C. Hochmuth, multi-County Extension agent, UF/IFAS Extension Suwannee County, UF/IFAS Extension, Gainesville, FL 32611.

The Institute of Food and Agricultural Sciences (IFAS) is an Equal Opportunity Institution authorized to provide research, educational information and other services only to individuals and institutions that function with non-discrimination with respect to race, creed, color, religion, age, disability, sex, sexual orientation, marital status, national origin, political opinions or affiliations. For more information on obtaining other UF/IFAS Extension publications, contact your county’s UF/IFAS Extension office.
U.S. Department of Agriculture, UF/IFAS Extension Service, University of Florida, IFAS, Florida A & M University Cooperative Extension Program, and Boards of County Commissioners Cooperating. Nick T. Place, dean for UF/IFAS Extension.

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