Why Do My Peppers Have Soft Sunken Spots?

When your peppers develop soft, sunken, discoloured spots — sometimes with mould or a dark, water-soaked look — a fungal fruit rot has taken hold. This is different from blossom end rot, which is a dry calcium disorder; here a real fungus is at work, usually moving in through damp conditions, a wound, or fruit touching wet ground. The fruit is the prize, so these rots are worth stopping. Let me help you identify and manage them.

Anthracnose: the common pepper fruit rot

The classic pepper fruit rot is anthracnose. It shows as circular, sunken, water-soaked spots on the fruit that enlarge and darken, often developing concentric rings and, in humid weather, a pinkish or orange ooze of spores in the centre. It can hit green or ripe fruit and spreads fast in warm, wet conditions. Affected peppers quickly become inedible as the soft rot spreads. The spores survive on debris and can be seed-borne, so it tends to return to the same beds.

Grey mould and soft rots

Other fungi and bacteria cause soft rots too. Grey mould (botrytis) produces a soft brown rot covered in fuzzy grey spores, often starting at a wound or the old flower scar. Various soft rots cause mushy, collapsing lesions, frequently entering through cracks, sunscald patches, or insect damage. Like anthracnose, these thrive where fruit and foliage stay damp and air is still. Any break in the pepper's skin is an open door for them.

How to manage and prevent

The strategy is the same regardless of which rot you have: keep things dry and remove sources of infection. Remove and bin affected fruit promptly — never compost it, and don't leave rotting peppers on the plant or soil where they shed spores. Water at the base in the morning, never overhead, so fruit and leaves dry fast. Improve airflow with generous spacing and by removing congested growth. Keep fruit from touching wet soil, and protect plants from sunscald (which creates entry wounds) by maintaining healthy leaf cover. Harvest promptly when ripe rather than leaving fruit to sit.

Preventing it next season

Because these fungi overwinter on debris and can travel on seed, prevention spans seasons. Start with clean, disease-free seed and resistant varieties where available. Rotate peppers to a fresh spot each year, and clear away all pepper and related debris at season's end. Mulch to reduce soil splash onto low fruit. Maintain the dry-leaf watering and good spacing from the start, before any disease appears. These steps, taken early, are far more effective than trying to halt a rot in full swing during wet weather.

The takeaway

Soft, sunken spots on peppers are fungal rots driven by moisture and wounds. Manage them by removing affected fruit, keeping fruit and foliage dry, improving airflow, and protecting the fruit from damage — and prevent them with clean seed, resistant varieties, rotation and end-of-season clean-up. Stay ahead of the damp and your peppers will stay sound and edible to harvest.