The sugarcane-to-bioethanol and soybean-to-biodiesel production processes were evaluated using robust energy metrics, namely, the change in energy quality and the change in energy yield. The biomass crops, in their entirety, were considered as the mass and energy inputs into the respective processes where the process efficiencies were evaluated. Process models were developed for the bioethanol and biodiesel upgradation processes using literature data. Various scenarios were explored that considered the amount of waste- and by-products used in cogeneration to produce process steam and electricity, as well the valorisation of lignocellulosic residues in second generation bioethanol production.