Increasing evidence supports the notion that in humans many pathological conditions including obesity, metabolic syndrome, and type 2 diabetes are closely related to the amount and quality of each nutritional component and to an impairment of the metabolic homeostatic mechanisms of their utilization. Cell signaling pathways that sense the availability of nutrients and the energy status of the cells communicate with signaling pahways triggered by hormones and growth factors to coordinately regulate whole-body metabolic homeostasis. The aim of this review is to provide an overview picture of current knowledge about the main molecular mechanisms that connect nutritional status, hormones, and nutrient levels with gene expression, metabolic homeostasis, and nutrient sensing. We recapitulate molecular mechanisms governing fuel selection between glucose and fatty acids in different nutritional conditions, highlighting metabolic flexibility as mechanism to ensure metabolic health. Disrupted metabolic flexibility, or metabolic inflexibility, is associated with many pathological conditions including metabolic syndrome, type 2 diabetes mellitus, and cancer. We also describe how macronutrients that can be used as energy sources may reciprocally modulate their own metabolism as well as directly interact with transcriptional factors, nutrient sensors and nutrient sensing pathways in order to achieve metabolic homeostasis.