Chopped chillies develop dark spots in storage due to enzymatic browning and oxidation, processes accelerated by exposure to air and moisture. These spots don't necessarily indicate spoilage, but they can affect the chilli's appearance and flavor.
When chillies are chopped, their cells are damaged, releasing enzymes like polyphenol oxidase (PPO). These enzymes react with phenolic compounds present in the chilli when exposed to oxygen in the air. This reaction leads to the formation of melanins, which are brown or black pigments. This is the same process that causes browning in apples or bananas. Moisture further accelerates this enzymatic activity. The higher the moisture content, the faster the browning reaction occurs. While the chillies may still be safe to eat, the dark spots can make them less appealing and may slightly alter their flavor profile, often making them taste more bitter. The rate of browning also depends on the type of chilli, with some varieties being more prone to it than others.
To minimize dark spots, store chopped chillies in an airtight container in the refrigerator. Adding a small amount of acid, like lemon juice or vinegar, can help inhibit the enzymatic browning process.