Biodiesel is commonly produced from lipid feedstock, animal fats and waste cooking oil by transesterification reaction. Considering the depletion of fossil fuel, biodiesel is gaining more attention as a renewable and environmental friendly fuel. The rapid growth of biodiesel industry thereafter has raised concerns to many existing commercial biodiesel enterprises. The major issues like feedstock flexibility, yield productivity and environmental impact are always the challenges to the continuous growth of conventional biodiesel processing technology. The processing of biodiesel is greatly hinged on the rich scientific background and technology development for better process advancement. The present paper reviews various concerns raised from the commercial biodiesel processing technology. It also addresses some innovative process intensification (PI) technologies, which likely bring appropriate technological improvement for biodiesel production.