Microbial oils are regarded as a sustainable alternative to vegetable oils for biodiesel manufacturing. However, in order to develop a cost-effective process, high-lipid producer microorganisms should be combined with low-cost renewable growth substrates. For this reason, the objective of the present study was to assess comparatively the oil-producing performance of 9 oleaginous fungi belonging to the Aspergillus, Mucor, Mortierella and Cunninghamella genera on three relevant and widespread waste, such as glycerol, orange peel extract (OPE) and ricotta cheese whey (RCW). This screening was performed at the shaken flask level and, among the strains under study, Mortierella isabellina NRRL 1757 turned out to be the most efficient and versatile and its lipid profile was found to be highly compatible with biodiesel production. Process transfer of M. isabellina lipid production to the lab-scale Stirred Tank Reactor on all the three waste-based media, was shown to be feasible, achieving a lipid productivity of 0.46, 1.24 and 0.91 g/(Ld) on glycerol, OPE and RCW, respectively. Noteworthy, the fatty acid analysis of the oils produced, confirmed their suitability for biodiesel manufacturing, exhibiting a high similarity to palm and Jatropha oils commonly used as feedstock for this production. (C) 2018 Published by Elsevier B.V. on behalf of Institution of Chemical Engineers.