The treatment of periprosthetic joint infections (PJI), and especially of re-infections, poses a highly complex problem in orthopaedic surgery. While fungal infections are rare, they present a special challenge. The therapy is often protracted and based on limited evidence. A total of 510 hip and knee revision surgeries were analysed for the occurrence of bacterial and fungal PJI. In patients with PJI, the duration of the hospital stay and the incidence of disarticulation of the infected joint were recorded. Out of the analysed revision arthroplasties, 43.5% were due to PJI. Monomicrobial infection occurred in 55.2%, dual microbial infection in 21.4%, and polymicrobial (≥3 different bacterial or fungal species) infection in 17.2% of the cases. Overall, Candida species were detected in 12.4% cases. Candida albicans was the main fungal pathogen. In 6.9% of cases, disarticulation of the joint was the only option to control PJI. The detection of polymicrobial infection more than doubled in follow-up revisions and there was a strong association between detection of Candida infection and disarticulation (OR 9.39). The majority of fungal infections were mixed infections of bacteria and Candida albicans. The choice of a biofilm penetrating antimycotic, e.g., caspofungin, together with a sufficient standard procedure for detection and surgical treatment can help to control the infection situation. Fungal infection often proves to be more difficult to treat than anticipated and is more frequent than expected.