The metabolism and function of trehalose as a compatible solute in Archaea was not well understood. This combined genetic and enzymatic approach at the interface of microbiology, physiology, and microbial ecology gives important insights into survival under stress, adaptation to extreme environments, and the role of compatible solutes in Archaea . Here, we unraveled the complexity of trehalose metabolism, and we present a comprehensive study on trehalose function in stress response in S. acidocaldarius . This sheds light on the general microbiology and the fascinating metabolic repertoire of Archaea , involving many novel biocatalysts, such as glycosyltransferases, with great potential in biotechnology.