Principal insect pests in India are the shoot-borer caterpillar, Diaphania caesalis; mealybugs. Nipaecoccus viridis, Pseudococcus corymbatus, and Ferrisia virgata, the spittle bug, Cosmoscarta relata, and jack scale, Ceroplastes rubina. The most destructive and widespread bark borers are Indarbela tetraonis and Batocera rufomaculata. Other major pests are the stem and fruit borer, Margaronia caecalis, and the brown bud-weevil, Ochyromera artocarpio. In southern China, the larvae of the longicorn beetles, including Apriona germarri; Pterolophia discalis, Xenolea tomenlosa asiatica, and Olenecamptus bilobus seriously damage the fruit stem. The caterpillar of the leaf webbers, Perina nuda and Diaphania bivitralis, is a minor problem, as are aphids, Greenidea artocarpi and Toxoptera aurantii; and thrips, Pseudodendrothrips dwivarna.
Diseases of importance include pink disease, Pelliculana (Corticium) salmonicolor, stem rot, fruit rot and male inflorescence rot caused by Rhizopus artocarpi; and leafspot due to Phomopsis artocarpina, Colletotrichum lagenarium, Septoria artocarpi, and other fungi. Gray blight, Pestalotia elasticola, charcoal rot, Ustilana zonata, collar rot, Rosellinia arcuata, and rust, Uredo artocarpi, occur on jackfruit in some regions.
The fruits may be covered with paper sacks when very young to protect them from pests and diseases. Burkill says the bags encourage ants to swarm over the fruit and guard it from its enemies.