Building materials can be exposed to microorganisms (mainly bacteria, fungi and algae) in almost every aqueous medium or damp environment, water being the indispensable condition for life development. The activity of microorganisms can be responsible for mineralogical, chemical and micro-structural damage to the material (biodeterioration). Deleterious effects can also concern the aesthetics of a building (proliferation of colored biological stains on façades and roofs) or the quality of indoor air (presence of microorganisms in damp buildings). However, microorganisms can also have positive effects (healing of materials) and their action is explored through the development of bio-based protective systems intended for building materials. In all cases, understanding interactions between building materials and microorganisms is an indispensable step toward the development of more sustainable, better quality, safer structures in many environments. This paper presents two examples where the action of microorganisms has-or is likely to have-strong impact on the durability and safety of concrete structures. The first example concerns the biodeterioration of concrete in agricultural and agro-food environments. The second example is that of the abiotic and biotic reactivity of nitrates in repository of intermediate-level long-lived nuclear wastes. The paper presents the approaches used to explore and understand the phenomenology of bio-geo-chemical interactions in these complex environments. These studies notably comprise the development of test methods and experimental pilots to enable these explorations to be carried out. Current shortcomings in the scientific literature and in the standardization environment are also highlighted.