Anaerobic biodigesters play a crucial role in enhancing animal waste management. However, the presence of pathogens in the biodigestion process poses a significant concern. Candida spp., a widespread fungus known for its opportunistic nature and adaptability to diverse environmental conditions, including reciprocal transmission between humans and animals, is one such pathogen of concern. Therefore, it is imperative to assess the virulence profile of Candida spp. originating from anaerobic biodigestion processes. Here we demonstrate that strains isolated from the biodigestion process of dairy cattle waste exhibit noteworthy virulence mechanisms, surpassing the virulence of clinical control strains. After we identified strains from affluent, effluent, and biofertilizer, we observed that all analyzed isolates produced biofilm. Additionally, a substantial proportion of these isolates demonstrated phospholipase production, while only a few strains exhibited protease production. Furthermore, all strains exhibited resistance or dose-dependent responses to amphotericin B and itraconazole, with the majority displaying resistance to fluconazole. In the in vivo test, we observed a significant correlation (p < 0.05) between the LT50 and biofilm formation as well as hyphae/pseudohyphae production. Additionally, some isolates demonstrated a quicker nematode-killing capacity compared to clinical controls. Our findings underscore the considerable pathogenic potential of certain Candida species present in the dynamics of anaerobic biodigestion. Importantly, the anaerobic biodigester system did not eliminate Candida strains from dairy cattle waste, highlighting the need for caution in utilizing biodigester products. We advocate for further studies to explore the virulence of other microorganisms in various animal production contexts. Furthermore, our results emphasize the urgency of enhancing waste treatment methods to effectively eliminate pathogens and curb their potential dissemination.