This work assessed the treatment of wastewater generated from three different industries viz., paper and pulp, biomass gasification and dairy by biodegradation followed by membrane filtration. Batch biodegradation was first carried out using wastewater as the potential substrate for oleaginous Rhodococcus opacus with lipid accumulation intracellular; subsequently, a microfiltration system was applied to recover the bacterial biomass grown as well as for residual chemical oxygen demand (COD) removal from the effluent. The combined process showed excellent results in terms of COD removal from the industrial wastewaters, with the values 56.8%, 46.1% and 68.9% for dairy, paper and pulp and biomass gasification wastewaters, respectively, by biodegradation. These values were further improved to 92.7%, 87.6% and 88.2%, respectively, following the microfiltration step performed by employing a low-cost ceramic membrane. In addition, lipids accumulated by the bacterium were extracted and characterized for biodiesel production potential. Lipid characterization using H-1 NMR confirmed the presence of saturated fatty acids. Gas chromatography analysis of the transesterified lipids revealed the presence of methyl palmitate and methyl stearate. In addition, the estimated properties of the transesterified product affirmed its potential for biofuel application.