Most of the energy harvested from food molecules is transferred to the electron transport chain by NADH and FADH₂.  As electrons move through the transport chain, hydrogen ions H⁺ are pumped from the matrix into the intermembrane space of the mitochondria.  This results in a high H⁺ concentration in the intermembrane space.  As a result of this gradient, H⁺ diffuse back into the matrix through ATPase.  This activates ATPase, which catalyzes the formation of ATP.

NADH activates 3 proton pumps and results in the production of
3 ATP.