The ability of the opportunistic yeast Candida albicans to acquire and maintain homeostatic levels of manganese (Mn), particularly in the metal-limited host environment, is an important determinant of its fitness. Although significant focus has been given to mechanisms of iron and copper acquisition and their roles in C. albicans fitness, little is known about how this yeast maintain and control Mn homeostasis. Here, we presented a comparative proteomic and phospho-proteomic analysis in C. albicans cells experiencing Mn starvation. Both proteome and phosphoproteome of the C. albicans reference strain SC5314 growing in Mn-depleted medium were compared to those of cells thriving in Mn-repleted medium. Samples were collected in four biological replicates at two time-points (5 and 90 min). LC–MS/MS identified approximately 1500 differentially abundant proteins and over 140 phosphorylated proteins.