The cell wall of fungi is a highly complex structure consisting of a network of polysaccharides in which a plethora of different proteins are embedded. It is one of the major organelles of the cell surrounding it like an armor which protects from environmental stresses like osmotic pressure and defines the shape and physical strength of the fungal cell. It is crucial for colonization and infection since it defines the interface between host and pathogen. No similar structure is present in the host, therefore it defines a prime target for drug development. In this context, it has been shown that cell surface proteins are required for adhesion to host cells. The fact, that both pathogenic fungi, like Candida albicans as well as non-pathogenic fungi, like Saccharomyces cerevisiae, in general, have a very similar polysaccharide structure but differ significantly in their protein composition which underscores the importance of cell wall proteins for pathogenesis. However, cell wall proteomics of fungi is a highly challenging task due to the complex biochemistry of these proteins. The extensive post-translational modifications and covalent attachment to the polysaccharide backbone of a large proportion of cell wall proteins makes it a demanding task to isolate and identify them. In this article, we describe the recent approaches that have been developed to describe cell wall dynamics and to isolate and identify cell wall proteins in the pathogenic yeast C. albicans.