Mitochondria are the powerhouses of eukaryotes and the main sites of ATP synthesis in cells performing aerobic respiration. Using the energy stored in an electrochemical proton gradient, the protein complex ATP synthase catalyses the conversion of ADP and inorganic phosphate to ATP, while complex I and the other respiratory chain complexes replenish the gradient. Efficient ATP synthesis is highly dependent on the interplay between these two components. By using electron cryo-tomography, we have determined the structure and organisation of these complexes in situ and demonstrated, contrary to standard textbooks, that these two components are spatially separated in mitochondrial cristae. In addition, through mutation studies, protein reconstitution experiments, and coarse grain molecular dynamics simulations we have shown that the ATP synthase has a fundamental role in the formation and shaping of mitochondrial cristae. These results, together with species-specific variations in the formation of ATP synthase dimers and respiratory chain supercomplexes will be discussed.