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Background: Synthetic algal–fungal and algal–bacterial cultures have been investigated as a means to enhance the technological applications of the algae. This inclusion of other microbes has enhanced growth and improved stress tolerance of the algal culture. The goal of the current study was to investigate natural microbial consortia to gain an understanding of the occurrence and benefits of these associations in nature. The photosynthetic protist Euglena mutabilisis often found in association with other microbes in acidic environments with high heavy metal (HM) concentrations. This may suggest that microbial interactions are essential for the protist’s ability to tolerate these extreme environments. Our study assessed the Cd tolerance of a natural fungal–algal–bacterial (FAB) association whereby the algae is E. mutabilis. Results: This study provides the first assessment of antibiotic and antimycotic agents on an E. mutabilisculture. The results indicate that antibiotic and antimycotic applications significantly decreased the viability of E. mutabiliscells when they were also exposed to Cd. Similar antibiotic treatments of E. graciliscultures had variable or non-significant impacts on Cd tolerance. E. gracilisalso recovered better after pre-treatment with antibiotics and Cd than did E. mutabilis. The recoveries were assessed by heterotrophic growth without antibiotics or Cd. In contrast, both Euglenaspecies displayed increased chlorophyll production upon Cd exposure. PacBio full-length amplicon sequencing and targeted Sanger sequencing identified the microbial species present in the E. mutabilisculture to be the fungus Talaromycessp. and the bacterium Acidiphilium acidophilum. Conclusion: This study uncovers a possible fungal, algal, and bacterial relationship, what we refer to as a FAB consortium. The members of this consortium interact to enhance the response to Cd exposure. This results in a E. mutabilisculture that has a higher tolerance to Cd than the axenic E. gracilis. The description of this interaction provides a basis for explore the benefits of natural interactions. This will provide knowledge and direction for use when creating or maintaining FAB interactions for biotechnological purposes, including bioremediation.