Frosty pod rot (FPR), caused by Moniliophthora roreri, is one of the most devastating diseases of cocoa plantations in the Americas. This hemibiotrophic fungus only infects the fruits of the cocoa tree. It reduces yields and devalues the fruits, consequently causing economic losses and compromising crops' socioeconomic potential. We analyzed the transcriptome of M. roreri spores and mycelium incubated in a cocoa fruit extract from susceptible plants. A total of 871 differentially expressed genes (DEGs) were identified in spores at different incubation times and in mycelium. The identified DEGs were found to be involved in several biological processes and molecular functions, among them oxidoreductase function, proteolysis, transcriptional regulation, binding processes and stress response. We also explored the repertoire of secreted proteins and putative effectors located in the apoplast and cytoplasm of the host, and found 1075 transcripts encoding secreted proteins, of which 61 were DEGs and 23 were putative effectors, associated with plant cell wall breakdown, oxidative stress, and carbohydrate metabolism. Data also revealed transcripts with up to 50-fold higher expression between the incubation times of non-germinated spores and mycelium, which are considered candidates for marker genes in fungal development. These molecules were related to functions such as growth, pathogenicity, kinase and oxidoreductase activity, playing important roles in the interaction of M. roreri and Theobroma cacao. Functional analysis of three candidate effectors revealed impacts on leaf morphology, mainly leaf drying and wilting, often culminating in necrosis. Our results expand the understanding of the molecular basis of how FPR affects host plants, in addition to identifying a set of secreted proteins that require functional characterization to contribute to disease control.