The present study reports on the characterization and validation of a 3D stochastic microsensor that utilizes nitrogen, and boron co-doped graphene for the simultaneous determination of p53, HER-3, and HER-4 in biological samples. The synthesis and morphological characterization of nitrogen, and boron co-doped graphene powder was conducted through the utilization of scanning electron microscopy and X-ray powder diffraction techniques. The utilization of the 3D stochastic microsensor based on nitrogen, and boron co-doped graphene for the assay of p53 demonstrated an increased sensitivity and an extended linear concentration range. The limits of quantification for all biomarkers tested were observed to be at the magnitude order of attogram ml−1. The outcomes derived from the application of the suggested stochastic microsensor demonstrated a significant association with biological samples, indicating the prospective dependability of this for screening examinations employed in the molecular identification and quantification of p53, HER-3, and HER-4 in samples of whole blood, gastric tissue tumors, saliva, and urine. The signatures of other biomarkers or substances found in biological samples were found to be higher than those of p53, HER-3, and HER-4, suggesting that the latter do not impede the measurements. The biomarkers demonstrate accurate identification in biological samples, achieving recoveries greater than 98.00% and RSD% values less than 0.05.