Bio diesel is considered a viable alternative to the use of diesel. Transmogrification is the most used method of bio diesel production and usually occurs in batch reactors and requires several minutes or hours to achieve high yield rates. However, this process has been recently tested in micro reactors. One of the most important elements of these micro reactors is the micro mixer, which should perform a quick and efficient mixing of reactants. Micro mixers with circular obstructions split and recombine the flow stream, increasing the interaction of chemical species. Therefore, we carried out numerical simulations of Atrophy carcass oil-ethanol mixing and reaction in micro mixers with circular obstructions. Three different micro mixers were investigated: T-channel, T-channel with circular obstructions and T-channel with alternate circular obstructions. A mixing study was conducted for Reynolds number ranging from 1 to 160 and residence times for reaction of 0.20–100 s. The T-channel with alternate circular obstructions showed the highest degree of mixing (0.99). The presence of obstacles improved the conversion of species. Maximum conversion was 99.07% (T-channel), 99.01% (T-channel with circular obstructions) and 99.09% (T-channel with alternate circular obstructions). The effectiveness of using channels with circular obstructions in bio diesel synthesis was numerically demonstrated.