Most pepper diseases present symptoms primarily on the leaves and stems. Two problems may cause spots to develop on fruit: bacterial spot and blossom-end rot.
Bacterial spot affects both peppers and tomatoes, causing fruits to become dotted with small brown lesions. Although a few treatments are available, they are not very effective, according to the University of Massachusetts Extension. Because the disease overwinters in plant debris, remove and destroy infected plants and rotate tomatoes and peppers to a new section of the garden next season to prevent reinfection.
Blossom-end rot produces brown, leathery patches on the ends of peppers and several other garden crops. These lesions invite secondary fungal infection. Calcium deficiency brought on by drought causes blossom-end rot, so providing adequate water treats and prevents the disease.
When distinguishing between the two diseases, examine the rest of the plant closely for lesions. Bacterial spot affects all above-ground plant parts, including leaves and stems. Blossom-end rot affects only one part of the fruit.