Development in every aspect interconnects society, economy, and environment. Significant advances in technology and industry have led to various environmental problems affecting ecosystems, climate, and biodiversity. We must face the challenge of the adjustment of industry and the progress of society to a clean environment. The framework of this article is built around imperatives given by the European Council through important documents related to environmental protection, climate change, and clean energy. In the European Green Deal, Horizon Europe, and EU partnership for R&I, researchers are given the benefit of the doubt to halt and remove pollution. In line with the EU Circular Talks platform that includes bioremediation as a new–old approach to dealing with pollution sustainably, the study aims to present substantive examples of the capacity of some microorganisms to remove toxic substances from the environment. Therefore, the study focuses on the determinants in native and engineered organisms. The article aims to provide biochemical data valuable in cleaning particular pollutants in vivo/in vitro, showing scientific data available to researchers and stakeholders. This paper aims to clarify the potential of in situ biological techniques and their application to remove different inorganic or organic contaminants in the environment.