Milk serves as a suitable medium for the growth of foodborne pathogens, including Candida albicans, which may possess virulence properties. Therefore, understanding the virulence characteristics and thermotolerance of C. albicans isolated from milk is important for ensuring safety and quality in the dairy industry. This study aims to identify Candida species in raw milk and detect thermotolerance and pH-changing features of C. albicans by indicating antifungal resistance, virulence and biofilm-forming capability via phenotypic and genotypic researching. Identification of Candida species and detection of antifungal resistance and virulence markers in C. albicans were carried out via Polymerase Chain Reaction. Thermal tolerance of C. albicans isolates was determined through microbial counts on specific parameters (63°C, 68°C and 72°C). Each experiment was replicated three times to ensure reliability. Post hoc analyses were performed to compare the observed differences. The prevalence of Candida albicans (15%), Candida parapsilosis (8%), Candida krusei (3%), Candida lusitaniae (2%) and Candida glabrata (1%) was revealed in 100 milk samples. C. albicans isolates exhibited significant virulence, antifungal resistance and biofilm-producing properties. Low-temperature long-time pasteurisation (63°C for 30 min) provided a 3.18 log reduction of C. albicans from an initial 4 log population, while high-temperature short-time pasteurisation (72°C for 15 s) resulted in a 0.83 log reduction. Determination of the thermotolerance of C. albicans with phenotypically and genotypically determined virulence properties will guide the optimisation of the pasteurisation process to prevent economic, safety and quality concerns in dairy industry. This investigation will also provide valuable insights into the scientific understanding of the dynamics of virulent C. albicans in milk and the efficacy of heat treatments in reducing its load.