Fe3O4 nanoparticles are one of the most promising candidates for biomedical applications such as magnetic hyperthermia and theranostics due to their bio-compatibility, structural stability and good magnetic properties. However, much is unknown about the nanoscale origins of the observed magnetic properties of particles due to the dominance of surface and finite size effects. Here we have developed an atomistic spin model of elongated magnetite nanocrystals to specifically address the role of faceting and elongation on the magnetic shape anisotropy. We find that for faceted particles simple analytical formulae overestimate the magnetic shape anisotropy and that the underlying cubic anisotropy makes a significant contribution to the energy barrier for moderately elongated particles. Our results enable a better estimation of the effective magnetic anisotropy of highly crystalline magnetite nanoparticles and is a step towards quantitative prediction of the heating effects of magnetic nanoparticles.