The preparation of graphene/apatite and graphene oxide/apatite hybrid nanocomposites has recently attracted great attention in the biomaterial community. The sitting drop vapor diffusion technique has been assessed as a preparative method for such nanocomposites in this work. The technique has been employed to induce heterogeneous nucleation and growth of calcium phosphate in the presence of exfoliated graphene and commercial graphene oxide flakes, both labeled with L-Alanine. Exfoliated multilayered graphene flakes were produced by sonication-assisted liquid-phase exfoliation of graphite. In both composites, the apatite nanocrystals displayed similar size and shape, but different labile and B-type carbonation contributions. Graphene and graphene oxide flakes also influenced the carbonation degree of the apatite, which was almost half that measured for the apatite blank, as well as the aggregation state of their composites. In this regard, those composites with graphene oxide formed larger aggregates because of their wider size distribution, with a high-volume percentage of nanosheets (of about 4 nm length). Overall, the method is very useful to prepare small amounts of nanocomposite with high reproducibility.