The mitochondrial ATP synthase (F₁–F₀ complex) of Saccharomces cerevisiae is a composite of different structural and functional units that jointly couple ATP synthesis and hydrolysis to proton transfer across the inner membrane. In organello, pulse labelling and pulse‐chase experiments have enabled us to track the mitochondrially encoded Atp6p, Atp8p and Atp9p subunits of F₀ and to identify different assembly intermediates into which they are assimilated. Surprisingly, these core subunits of F₀ segregated into two different assembly intermediates one of which is composed of Atp6p, Atp8p, at least two stator subunits, and the Atp10p chaperone while the second consists of the F₁ ATPase and Atp9p ring. These studies show that assembly of the ATP synthase is not a single linear process, as previously thought, but rather involves two separate but coordinately regulated pathways that converge at the end stage.