Palm empty fruit bunches (EFB) were valorized into fungal lipids by oleaginous fungus Aspergillus tubingensis TSIP9 under solid-state fermentation (SSF) and submerged fermentation (SmF). An integrated SSF-SmF process increased lipid production from 116.2 ± 0.1 mg/g-EFB under SSF and 60.1 ± 0.2 under SmF up to 124.9 ± 0.5 mg/g-EFB, possibly due to the combined benefits of dispersed mycelia forming during SSF and better mass transfer during SmF. As A. tubingensis lacks sufficient β-glucosidase, it was co-cultured with high β-glucosidase-producing Trichoderma reesei QM 9414. The co-cultures improved overall lipid yields likely due to synergistic interaction of the two fungi. After inoculum size was optimized and the co-cultures were performed in bioreactors, the lipid yield was increased up to 205.1 ± 1.1 mg/g-EFB. The fatty acid composition of fungal lipids indicated their potential use as biodiesel feedstocks. The fungal fermentation of EFB also provided cellulose pulp residues. These strategies could be practical options for low-cost biovalorization of biomass wastes.