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The human fungal pathogen Candida albicans possesses two genes expressing a cyanide-insensitive Alternative Oxidase (Aox) enzymes in addition to classical and parallel electron transfer chains (ETC). In this study, we examine the role of Aox in C. albicans under conditions of respiratory stress, which may be inflicted during its interaction with the human host or co-colonising bacteria. We find that the level of Aox expression is sufficient to modulate resistance to classical ETC inhibition under respiratory stress and are linked to gene expression changes that can promote both survival and pathogenicity. For example we demonstrate that Aox function is important for the regulation of filamentation in C. albicans and observe that cells lacking Aox function lose virulence in a zebrafish infection model. Our investigations also identify that pyocyanin, a phenazine produced by the co-colonising bacterium Pseudomonas aeruginosa, inhibits Aox-based respiration in C. albicans. These results suggest that Aox plays important roles within respiratory stress response pathways which C. albicans may utilise both as a commensal organism and as a pathogen.