This paper demonstrates the excellent temperature control and rapid equipartioning of the kinetic energy of the massive generalized Gaussian moment thermostat (MGGMT, one thermostat is coupled to each degree of freedom) in isothermal density functional molecular dynamics (MD) simulations on the Born-Oppenheimer potential energy surface. The MGGMT is implemented in the DMol 3 approach and, as far as we know, it is the first time in literature that the MGGMT is combined with density functional methods. The performance of the MGGMT approach is illustrated with MD simulations of the iron porphyrin-imidazole-carbon monoxide [FeP(Im)(CO)] complex and compared with constant energy MD simulations on the same system. Both MD approaches lead to similar average structures of the FeP(Im)(CO) complex. The examination of the frequency distribution functions reveals that the structural dynamics are not seriously affected by the dynamics of the parameters introduced by the MGGMT. The equipartitioning rates in the MGGMT simulations are significantly faster than in the constant energy simulation. We recommend the MGGMT approach as an very efficient equilibration technique in MD simulations and it emerges as a useful technique for, e.g., simulated annealing and non-equilibrium MD simulations.