The wild strain of Mucor circinelloides URM 4182 from a Brazilian culture collection was previously recognized as potential oleaginous microorganism that supplied single cell oil (SCO) with suitable properties for biodiesel synthesis. This work focused on assessing the accumulation of storage lipid by this strain grown in various media containing different carbon sources and the subsequent conversion of the microbial lipids into biodiesel. The chosen carbon sources can be obtained from several agro-industrial residues such as sucrose and fructose (sugarcane molasses), xylose (hydrolysate of lignocellulosic materials like sugarcane bagasse), starch (corn milling), ethanol and glycerol (byproducts from biodiesel production). The carbon source was found to influence the obtained fatty acid profile of M. circinelloides oil, realizing important attributes that favor its use for biodiesel production, including good levels of saturated (Cn: 0) and monounsaturated (Cn: 1) fatty acids. Polyunsaturated fatty acids with two (linoleic acid) or three double (linolenic acid) bonds were also found, but their concentrations decreased from 33.2 to 19.8% when glucose was replaced by a substrate based on sucrose. The feasibility of using low-cost feedstocks in the synthesis of microbial lipids was demonstrated, with the exception of ethanol that inhibited fungal growth. The lipid-bearing biomass was then subjected to direct transesterification using a robust solid acid catalyst (12-molybdophosphoric acid supported on alumina) in a high-pressure reactor, producing ethyl esters as biodiesel material with very high conversion yields (98.5%) and minor levels of byproducts.