Understanding the biomolecular interactions between graphene nanomaterials and human cells is a prerequisite for the utilization of graphene-based nanomaterials as a diagnostic or therapeutic tool. Currently, the impact of exposure to graphene and its derivative graphene oxide (GO) on the immune system remains elusive. To characterize the complex interactions between graphene nanomaterials and immune cells, we propose an integrative analytical pipeline encompassing the evaluation of molecular and cellular parameters. Single-cell mass cytometry was used to dissect the effects of GO flakes and GO flakes functionalized with amino groups on 15 immune cell populations, interrogating 30 markers at the single-cell level. Next, we integrated single-cell mass cytometry with genome-wide transcriptome analysis and we concluded that the amine groups reduce the perturbations caused by GO on cell metabolism and increase biocompatibility. Moreover, GONH2, but not GO, polarizes T-cell and monocyte activation toward a T helper-1/M1 immune response. These observations support the implementation of nanoscale platforms for immunotherapy, as vaccine carrier and nano-adjuvant. This study describes an innovative approach for the comprehensive analysis of nanomaterial interactions with distinct immune cells, laying the foundation for the incorporation of single-cell mass cytometry for the characterization of nanomaterial-immune cell interactions.