We report here the charge transport behavior in graphene nanojunctions in which graphene nanodots, with relatively long relaxation time, are interfaced with ferromagnetic electrodes. Subsequently we explore the effect of substitutional doping of transition metal atoms in zigzag graphene nanodots (z-GNDs) on the charge transport under non-collinear magnetization. Only substitutional doping of transition metal atoms in z-GNDs at certain sites demonstrates the spin filtering effect with a large tunnelling magnetoresistance as high as 700%, making it actually suitable for spintronic applications. From the electrical field simulation around the junction area within the electrostatic physics model, we find that the value of electric field strength increases especially with doped graphene nanodots, as the gap between the gate electrode and tip axis is reduced from 3 nm to 1 nm. Our detailed analysis further suggests the onset of asymmetric Coulomb oscillations with varying amplitudes in graphene nanodots, on being doped with magnetic ions. Such kind of tunability in the electronic conductance can potentially be exploited in designing spintronic logic gates at nanoscale. (c) 2017 Elsevier B.V. All rights reserved.