The bacterium, Pseudomonas aeruginosa, and the fungus, Candida albicans, commonly co-infect the lungs of Cystic Fibrosis patients, and the surfaces of surgical and burn wounds. Both species form extensive, structured biofilms on the surfaces of mucosa and medical devices. The main objective of this research was to determine whether P. aeruginosa–C. albicans biofilm interactions impact antimicrobial tolerance. Antimicrobial susceptibilities of single- and dual-species biofilms were investigated using an in vitro biofilm assay, and biofilms were visualised using a range of microscopy techniques. Dual-species RNA sequencing of biofilm cells revealed transcriptional changes during P. aeruginosa–C. albicans biofilm interactions. The data show that C. albicans protects P. aeruginosa biofilm cells from the effects of meropenem. We propose that this protection is likely mediated by fungal extracellular matrix polysaccharides, specifically mannan and ß-glucan, and potentially also via adhesion of P. aeruginosa cells to C. albicans hyphae. Conversely, P. aeruginosa potentiates the activity of amphotericin B against C. albicans biofilm cells. With support from the dual-species transcriptomic data, we propose that this occurs as a result of P. aeruginosa secreted phenazines, which lead to oxidative stress in C. albicans cells. These findings have direct clinical implications for the treatment of co-infected patients.