The charge transport through ferrocene 1,1′‐diamine (FDA) molecules between gold electrodes is investigated using the mechanically controllable break junction technique combined with a theoretical framework of density functional theory simulations to understand the physics of these molecular junctions. The characteristic conductances of the molecule are measured at low bias as well as current–voltage (IV) characteristics. By fitting the IV characteristics to the single‐level model, the values for the position of the molecular level, mainly responsible for the transport, and its coupling to the leads, are obtained. The influence of the binding sites, molecular conformation, and electrode distance are systematically studied from a theoretical perspective. While a strong dependence of conductance on the adsorption geometry is found, the decrease of conductance as a function of electrode distance arises mainly from a decrease of coupling strength of the molecular electronic orbitals through a reduced overlap and, to a lesser extent, from a shift of their alignment with respect to the Fermi energy.