The world's citriculture has witnessed large-scale productivity decay due to microbial infections. The specialized metabolites produced during infection by pathogens are an important aspect of complex phytopathogen–host interactions and can be crucial for virulence and disease viability. In this review, we comprehensively explore microbial natural products produced during infection by the following citrus pathogens: Penicillium digitatum , Penicillium italicum , Penicillium citrinum , Aspergillus flavus , Fusarium solani , Alternaria alternata , Alternaria citri , Pseudomonas syringae , Elsinoë fawcettii , and Elsinoë australis . Additionally, we list the major microbial citrus diseases distributed worldwide and highlight the lack of consistent knowledge concerning the specialized metabolites that could play significant roles in some of the most important citrus diseases, such as Huanglongbing, citrus canker, citrus variegated chlorosis, citrus tristeza virus, citrus sudden death, sour rot, anthracnose, and citrus black spot.