A consolidated biorefinery was developed using spent coffee grounds (SCGs) and orange peel residues (OPR) to produce microbial oil and value-added co-products. Coffee oil and antioxidant-rich extracts were initially extracted from SCGs. Free sugars and pectin-rich extracts were obtained from OPR. Microbial oil production was evaluated using various oleaginous yeast strains cultivated in commercial carbon sources. Microbial oil production was demonstrated in 30 L bioreactor scale using combined OPR-SCGs hydrolysate resulting in 56.7% (w/w) intracellular lipid accumulation and 0.32 g/(L∙h) productivity, corresponding to 68.1 g microbial oil production per 1 kg SCGs and 360 g OPR. Principal Component Analysis has been carried out to assess the similarity of microbial oil produced in this study and literature-cited oils considering the fatty acid methyl ester content. The biodiesel properties estimated based on predictive equations showed that they generally conformed with the limits set by European standards.