Increased use of implanted medical devices, use of immunosuppressants and an ageing population have driven the rising frequency of fungal biofilm-related diseases. Fungi are now recognized by the World Health Organization (WHO) as an emergent threat to human health, with most medically important species defined as critical or high-priority organisms capable of forming biofilms. Although we strive for a better understanding of diagnostic and therapeutic approaches to detect and treat these fungal diseases more generally, the issue of hard-to-treat biofilms is an ever-increasing problem. These are communities of interspersed cells that are attached to one another on a surface, such as a catheter, or trapped into a cavity such as a paranasal sinus. Biofilms are difficult to detect, difficult to remove and intrinsically tolerant to most antifungal agents. These factors can lead to devastating consequences for the patient, including unnecessary morbidity and mortality, need for reoperations and prolonged hospital stay. This Review describes the breadth and growing impact fungal biofilms have on patient management and explains the mechanisms promoting biofilm formation, focusing on how targeting these can improve therapeutic options.