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 phosphoproteomic study of B. cinerea, aimed to analyze the phosphoprotein 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). A total of 2854 and 2269 different phosphosites (2883 and 1137 phosphopeptides) were identified in glucose and TCW respectively, which map to 1338 phosphoproteins in glucose and 733 in TCW. Out of the identified phosphoproteins, 173 were exclusively found when glucose was the only carbon source and 11 when the carbon source was TCW. Differences in the pattern of phosphorylation-sites were also detected according to the carbon source. Gene ontology classification of the identified phosphoproteins showed that most of the characteristic proteins of the different carbon sources were related to signaling and transmembrane transport, thus highlighting the importance of these processes in the fungal adaptation to the surrounding conditions.