Microbial reduction of soluble selenium (Se) or tellurium (Te) species results in immobilization as elemental forms and this process has been employed in soil bioremediation. However, little is known of direct and indirect fungal interactions with Se-/Te-bearing ores. In this research, the ability of Phoma glomerata to effect transformation of selenite and tellurite was investigated including interaction with Se and Te present in sulfide ores from the Kisgruva Proterozoic volcanogenic deposit. Phoma glomerata could precipitate elemental Se and Te as nanoparticles, intracellularly and extracellularly, when grown with selenite or tellurite. The nanoparticles possessed various surface capping molecules, with formation being influenced by extracellular polymeric substances. The presence of sulfide ore also affected the production of exopolysaccharide and protein. Although differences were undetectable in gross Se and Te ore levels before and after fungal interaction using X-ray fluorescence, laser ablation inductively coupled plasma mass spectrometry of polished flat ore surfaces revealed that P. glomerata could effect changes in Se/Te distribution and concentration indicating Se/Te enrichment in the biomass. These findings provide further understanding of fungal roles in metalloid transformations and are relevant to the geomicrobiology of environmental metalloid cycling as well as informing applied approaches for Se and Te immobilization, biorecovery or bioremediation.