Chilli pepper: dark sunken patch at the bottom of a fruit

What it is likely to be on chilli pepper

1. Blossom end rot

   Candidate 1very common on this plant

   ·source

   Sourced guidancehigh confidence

   • Royal Horticultural Society: Blossom end rot
   • Home and Garden Information Center — Clemson Cooperative Extension: Blossom end rot of tomato and pepper

   Checked 2026-08-13

   A dark, sunken, leathery patch at the flower end of a fruit. It is not a disease and nothing is attacking the plant: the fruit could not move enough calcium into its fastest-growing tissue while it was forming, almost always because water supply was irregular.

   Points towards it

   • · it is overwhelmingly a container and growbag problem, because the whole root system is in a few litres of compost that dries and rewets sharply
   • · the fruit cannot get calcium when the plant cannot move water, so a pot that has been allowed to dry out between waterings is the mechanism
   • · a hot spell increases demand faster than a small root zone can supply, which is why the first fruit of a heatwave is the one affected
   • · it affects particular fruit — usually the earliest and the largest — rather than everything on the plant, because each fruit takes its calcium during its own swelling

   Argues against it

   • · a plant standing in water has a root problem rather than a supply problem, though the two can end up looking similar
   • · grey fuzz on the patch means a fungus has taken it, which is a different first cause even where rot followed

   Check this next

   Press the patch with a fingertip and then cut the fruit in half. Blossom end rot is a flat or sunken patch at the blossom end — the bottom, away from the stalk — that is leathery, dry and firm rather than soft, and inside the flesh beneath it is brown and dry through to the middle. It has no mould on it unless something else has moved in afterwards. Then look at the rest of the truss: the affected fruit are usually the earliest and biggest, and later ones on the same plant come out perfect once the watering is steady.

   What to do now

   Water steadily rather than more — this is a transport problem rather than a shortage, so calcium feeds and eggshells do nothing. Keep the compost evenly damp and never let a growbag or pot dry right out between waterings; a self-watering tray or a daily routine in hot weather is worth more than anything applied. Pick off the affected fruit so the plant stops carrying them. Larger containers and mulched compost surfaces both help, and the fruit that set after the watering steadies will be sound.

   ·source

   Sourced guidancehigh confidence

   • Royal Horticultural Society: Blossom end rot — control
   • Home and Garden Information Center — Clemson Cooperative Extension: Blossom end rot — management

   Checked 2026-08-13

2. Grey mould

   Candidate 2occasional on this plant

   ·source

   Sourced guidancemoderate confidence

   • Royal Horticultural Society: Grey mould (botrytis)
   • Agriculture and Horticulture Development Board — AHDB: Protected crops — botrytis

   Checked 2026-08-13

   Soft fruit turning brown and collapsing under a fuzzy grey coat, often overnight in wet weather. It is the single biggest cause of strawberry losses in a wet British summer, and it infects at flowering rather than when the mould appears.

   Points towards it

   • · peppers are grown in a closed greenhouse or conservatory where still humid air suits the fungus and there is no wind to dry the fruit
   • · grey furry growth on a soft brown patch is the fungus itself rather than a symptom of it
   • · damp compost and damped-down paths keep the air humid enough for it to establish
   • · it takes fruit at any stage and often gets in through damage or a scar rather than choosing an age

   Argues against it

   • · a bone-dry plant in dry air is not going to carry botrytis, and its fruit patches are the disorder instead
   • · moving air outdoors dries the fruit surface and makes it much less likely

   Check this next

   Press the patch and look for fuzz at the edge of it. Botrytis on a pepper makes a soft, watery brown patch that gives under a finger and carries grey furry growth around its margin in humid weather, and it usually starts where the fruit was damaged, split or touching a leaf. Blossom end rot is dry, firm and leathery with no growth on it, and it sits squarely at the blossom end. The two feel completely different through the skin, which is the quickest test available.

   What to do now

   Pick off and bin every affected fruit as soon as you see it — the spores come from what is already rotting, so leaving one on the plant is what infects the next. Ventilate the greenhouse day and night in damp weather rather than damping down, space the plants so air moves between them, remove the lowest leaves, and water the compost in the morning rather than the evening. Handle the fruit carefully at picking, since it enters through damage more often than through sound skin.

   ·source

   Sourced guidancehigh confidence

   • Royal Horticultural Society: Grey mould — control
   • Agriculture and Horticulture Development Board — AHDB: Protected crops — humidity management

   Checked 2026-08-13

3. Natural fruit colouring

   May be normalcommon on this plant

   ·source

   Sourced guidancemoderate confidence

   • Royal Horticultural Society: Chillies and peppers — growing
   • OSU Extension Service — Oregon State University: Peppers — fruit ripening and colour

   Checked 2026-08-13

   The dark purple, brown or near-black stage that many chilli and sweet pepper cultivars pass through on the way from green to their final colour. It usually starts as a patch at the blossom end or on the shoulder facing the sun, spreads over the fruit, and then gives way to red, orange or yellow. The flesh under it is firm and normal, which is what separates it from everything that is actually wrong.

   Points towards it

   • · a fruit changing colour on a healthy plant with nothing else happening is doing what the cultivar does
   • · every fruit of the same age on the plant does the same thing at the same time, which no disease and no disorder manages
   • · a well-watered plant in good condition is the case where the ripening explanation is likeliest and the disorder least likely
   • · strong light brings the pigment out, so a sunny bench or a sheltered outdoor spot both do it

   Argues against it

   • · a plant that has been drying out between waterings is exactly the one that gets blossom end rot, and that changes which explanation to prefer
   • · a ripening fruit changes colour in its own skin and grows nothing on the surface, so visible fungal growth rules the explanation out rather than merely weakening it — this rules it out entirely.

   Check this next

   Feel the patch, then wait a week. A ripening fruit is firm right up to the dark area and the surface is flat and smooth with the rest of the skin — no dent, no leathery texture, nothing to press into — and within a fortnight the red or orange comes through from underneath. Blossom end rot is sunken and leathery and never turns red. Look at the whole plant too: if every fruit of the same age is darkening in the same place, that is a cultivar characteristic, because a disorder picks individual fruit.

   What to do now

   Leave the fruit on the plant and look again in a week or two, which is the whole of the answer. Many varieties — jalapeño, Hungarian hot wax, and anything sold as a purple or chocolate pepper — pass through a dark stage as standard, and picking at that point simply gives a fruit that is not at its best. If you want certainty now, cut one fruit across: firm pale flesh right up to the skin means it is ripening, and brown dry flesh under the patch means it is not.

   ·source

   Sourced guidancehigh confidence

   • Royal Horticultural Society: Chillies and peppers — harvesting
   • OSU Extension Service — Oregon State University: Peppers — harvest maturity

   Checked 2026-08-13

Narrow it down

This page lists everything at once, which is the right shape for reading and the wrong shape for deciding. The interactive tool asks one question at a time, starting with whichever would separate these causes fastest, and stops as soon as further answers would not help.

Opens with the plant and the symptom already set. Nothing you answer is stored or sent anywhere — the answers live in the address bar and nowhere else.

What this does not cover

These are the causes GrowingHQ holds rules for on chilli pepper — not every cause there is. Where several problems look alike, the honest answer is often that they cannot be told apart by eye, and a page that named one would be guessing. If none of the above fits, the general dark sunken patch at the bottom of a fruit page lists causes across all plants, and the Chilli pepper profile lists the problems it is prone to.