The phytopathogen Botrytis cinerea is a ubiquitous fungus with a high capacity to adapt its metabolism to different hosts and environmental conditions in order to deploy a variety of virulence and pathogenicity factors and develop a successful plant infection. Here we report the first comparative phosphomembranome study of B. cinerea, aimed to analyze the membrane phosphoproteins composition of the fungus and its changes under different phenotypical conditions induced by two different carbon sources as plant based elicitors: glucose and deproteinized tomato cell wall (TCW). Proteomics analysisof membrane phosphoproteins was carried out by mass spectrometry. A total of 1115 proteins were successfully identified. Further analyses showed significant differences in the phosphomembranome composition depending on the available carbon source: 64 proteins were exclusively identified or overexpressed when the fungus was cultured with glucose as a sole carbon source, and 243 proteins were exclusively identified or overexpressed with TCW. GO and KEGG enrichment and clustering interaction analysis revealed changes in the composition of phosphomembranome with increase of autophagy in glucose conditions and protein degradation process, unfolded protein response (UPR) and ribosome biogenesis in TCW conditions.