The need to replace fossil fuels with biofuels has become necessary due to increasing release of greenhouse gases and particulate matter by combusting fossil fuels. Biofuels are better options compared to fossil-based fuels due to the availability of cheap and abundant renewable feedstock. Due to large number of possible fuel structures clustered in databases, solo experimental search strategies cannot identify a clean and efficient fuel molecule, and application of computer-aided approaches are necessary with integration of product and production design for fuel molecules of single- and multi-species, mass- and energy-based production pathway screening for costs, and emission estimation models. Optimization of biofuel production processes can surge fuel availability and development of surrogate fuel formulation and property modelling that would improve combustion efficiency of fuels in the engine infrastructure. In this review, we have taken more synergetic approach and analysed the microbial biofuel production processes utilizing 1) metabolic engineering tools on diverse microbes 2) chemo-catalytic pathways and 3) fuel design manoeuvre that is attracting much attention, and thus are extensively discussed in this review. The review emphasized that the utilization of new/modern chemo-catalytic refunctionalization of fuel molecules using new catalysts and enzymes have not only enhanced fuel yields but have led to the production of various novel advanced energy molecules from biomasses and microbes. The contribution of this review is that it highlights the current status of microbial fuels, metabolic engineering, fuel design and production of tailored made fuels, and potential future applications of microbial fuels in transport and energy sectors.