During the MOVPE growth of III-V layers on Ge substrates, Ge atoms can be evaporated or etched from the back of the wafer and reach the growth surface, becoming incorporated into the epilayers. This is the so-called Ge autodoping effect, which we have studied through a set of growth experiments of GaInP and Ga(In)As layers lattice matched to Ge substrates, which have been characterized by Secondary Ion Mass Spectroscopy. The role of V/III ratio and growth rate on Ge autodoping has been studied and a MOVPE reactor pre-conditioning prior to the epitaxial growth of III-V semiconductor layers that mitigates this Ge autodoping has been identified. In addition, the use of 2-inch versus 4-inch Ge substrates has been compared and the use of a Si3N4 backside coating for the Ge substrates has been evaluated.