The natural environment puts microorganisms in situations that are far different from those utilized for their characterization in the laboratory. Among the different aspects of the physiology that are altered, both the biotic and abiotic components of the environment modify the quorum sensing systems, which allow the coordination of the gene expression of a microbial population through chemical signaling. The modification of the quorum sensing activity can be exerted directly through the components of the signaling systems (i.e., the signal itself or the signal receptor) or indirectly through other cellular components. The understanding of the quorum sensing phenomenon in situ is highly relevant for a better exploitation of the microbial resources. In the case of plant-associated bacteria, the study of quorum sensing in planta has an additional interest in the agronomical importance of these microorganisms. However, beyond the significant progress of this research field at a molecular level, several important questions remain open about the quorum sensing activity for both beneficial and pathogenic bacteria when the natural environment is present.