Fungi have been an essential component of fundamental geological processes commonly called as geomycology emphasizing the importance of fungi in various processes. These processes include transformations (organic and inorganic), element cycling, and rock and mineral breakdown. Apart from this, many biological processes involving fungi include bioweathering, fungal-clay interactions, fungal-metal interactions, fungi-mediated mineral formations, etc. These processes have significance for environment and environmental biotechnology like bioremediation, climate change, etc. Although biotransformations take place both in aquatic and terrestrial ecosystems, it is more profound and studied in the latter system than in the former. In terrestrial system, it is particularly studied in soil, rock surfaces, and plant root–soil interface. These fungal-influenced geochemical processes have a great impact on the plant productivity and mobility of toxic elements. Some of these bioprocesses have beneficial applications in environmental biotechnology like metal leaching, recovery and detoxification, and xenobiotic and organic pollutant degradation. They may also result in adverse effects like degradation of building materials, stone and concrete. The morpho-molecular diversity of various fungi involved in bioweathering is an essential domain requiring more work. This would not only help to understand the bioweathering processes but also help to isolate and identify fungi useful for bioleaching, recovery of metals, bio fertilizer for nutrient deficient soils and degradation of monuments made of rocks. The application of omics to study the bioweathering fungi has also helped to understand new insights on them.