Flexi Says: Stage three of cellular respiration is the use of NADH and FADH2 to generate ATP. This occurs in two parts. First, the NADH and FADH2 enter an electron transport chain, where their energy is used to pump, by active transport, protons (H+) into the intermembrane space of mitochondria. This establishes a proton gradient across the inner membrane. These protons then flow down their concentration gradient, moving back into the matrix by facilitated diffusion. During this process, ATP is made by adding inorganic phosphate to ADP. Most of the ATP produced during cellular respiration is made during this stage.