Exudation of mucilage from pinhead-sized boreholes in cocoa pods was recorded in Karnataka, India, during 2021. Further investigations showed the association of scolytine beetles with infested pods. The identity of the pest, Xylosandrus crassiusculus, was confirmed through morphological characterization and sequencing of the mitochondrial COI gene. We studied the predisposing factors for its infestation, visible and concealed damaging symptoms, and fungal symbionts. In addition to its well-known symbiotic fungus, Ambrosiella roeperi, a new association of yeast, Ambrosiozyma monospora, was discovered. We also traced the possible role of the mirid bug, Helopeltis theivora, in host selection by X. crassiusculus. Overall results indicated that a ‘mirid bug-ambrosia beetle–pathogen complex’ is responsible for the severe damage to cocoa pods in South India.