This study focuses on the potential of four lipogenic yeasts to produce lipids using glycerol as carbon substrate; Candida molendinolei MH267796, Meyerozyma caribbica MH267795 and Rhodotorula minuta MH267794 were isolated from olive oil mill wastewater, while Cryptococcus curvatus ATCC20509 was used as control strain. Lipid production with crude glycerol was higher than that provided with pure glycerol. Fed-batch bioreactor cultures with M. caribbica MH267795 led to the production of 42.12 g L−1 of total dry weight with a microbial oil content of 48.14% (w w−1). In general terms, tested biodiesel properties meet all the limits set by European biodiesel standard UNE 14214:2013, excepting fatty acid methyl ester content. In addition, M. caribbica MH267795 oil biodiesel depicts a fatty acid methyl ester content (90.2% (w w−1)) higher than that of the most intensively studied C. curvatus oil biodiesel. Re-use of crude glycerol as raw material in biodiesel industry has been proven through fermentation, increasing potential full-scale application of such alternative.