During heavy ion collisions, high temperatures and strong magnetic fields are generated. We employ the gauge-gravity duality to study the N-f = 2 QCD phase diagram under these extreme conditions in the quenched approximation; in particular we use the non-antipodal Sakai-Sugimoto model (SSM). We take the different coupling of up and down flavors to the magnetic field into account geometrically, resulting in a split of the chiral phase transition according to flavor. We discuss the influence of the magnetic field on the chiral temperatures-in physical GeV units-in terms of the choice of the confinement scale in the model, extending hereby our elsewhere presented discussion of fixing the non-antipodal SSM parameters to the deconfinement phase. The flavor-dependent (T, L, eB) phase diagram, with variable asymptotic brane-antibrane separation L, is also presented, as a direct generalization of the known (T, L) phase diagram of the non-antipodal SSM at zero magnetic field. In particular, for sufficiently small L we are probing a Nambu-Jona-Lasinio (NJL)-like boundary field theory in which case we do find results very reminiscent of the predictions in NJL models