Magnetic nanoparticles as inert materials were excited under magnetic field to intensify transformation of soybean oil into fatty acid methyl ester (FAME) for biodiesel production. Experiments were carried out in four types of micromixers namely pitted mixing channel- T junction(PMT), pitted mixing channel-without junction (PMW), ring shaped mixing channel- T junction (RST) and ring shaped mixing channel- without junction (RSW). Synthesized Fe3O4 nanoparticles were employed. Two types of magnetic field, i.e., static (SMF) and rotating magnetic field (RMF) were created using permanent magnets. The results depicted that the values of FAME content under RMF were higher compared with those of SMF. The effect of rotational speeds(Omega) of magnets in RMF was assessed, and by increasing Omega, measurable enhancement of FAME content (wt.%) was seen. In addition, at Omega = 30 rad/s, the effects of RMF with two different arrangements of magnets (A1 and A2) on FAME content (wt.%) were investigated. A1 and A2 arrangements were chosen as efficient cases for pitted and ring shape micromixers, respectively. The effect of different nanoparticles concentrations on FAME content under efficient arrangements of RMF was evaluated. Maximum FAME content of 98.1% for PMT and 94.3% for RST were achieved in RMF layouts and MNPs concentration of 0.01 (w/v).