The endo-lysosomal system is essential to acquire lipids and nutrients according to the need of the cell and, subsequently, to maintain metabolic homeostasis. The strong connection between the endo-lysosomal system and metabolism is reflected in the observations that defects in this system are correlated with cardio-metabolic disorders, such as cardiovascular disease, type 2 diabetes and non-alcoholic fatty liver disease. The molecular mechanisms that interconnect the endo-lysosomal system with metabolism are, however, poorly understood. This can be largely explained by the fact that (1) endo-lysosomal and metabolic research are carried out independent of each other and (2) the number of model systems to study endo-lysosomal processes at an organismal and clinical level are limited. It is the ambition of EndoConnect to change this by bringing top scientists and industrial partners together to train early stage researchers in interdisciplinary research, with the focus on translating key findings from cellular and animal models to patients with cardio-metabolic diseases. It is our mission to: (1) understand the molecular organization and regulation of endo-lysosomal processes, (2) elucidate how metabolism and endo-lysosomal processes are intertwined, (3) understand how defects in the endo-lysosomal system contribute to the development of cardio-metabolic diseases and, finally, (4) how the endo-lysosomal system contributes to the efficiency of therapeutics. EndoConnect will provide an international training program for early stage researchers to acquire knowledge and state-of-the-art scientific, technical, and transferable skills to connect molecular and cell biology research with physiology and biomedical research towards translation. We expect that EndoConnect will increase our understanding of the molecular interrelation of the endo-lysosomal system with cardio-metabolic diseases, which will pave the road for novel diagnostics and therapeutics.