DNA-conjugated gold nanoparticles (AuNPs) were developed to target intracellular miRNA-16-5p across various cancer cell models by base pair complementarity. The Au-nanoprobe uptake was addressed by multiparametric mass cytometry (CyTOF) monitoring iridium and gold, enabling discrimination among Au nanoprobes in intact cells and cellular debris. Our findings reveal significantly higher incorporation in lung cancer (A549) and melanoma (A375) cells compared to hepatic (HepG2) and ovarian (A2780) models with particle numbers ranging from 200 to 1 AuNPs per cell, respectively. The internalized Au nanoprobes targeting miR-16-5p were captured by mixing the lysed cells with a half-complementary DNA probe immobilized on streptavidin-coated magnetic microparticles. By counting the Au events in the captured solution is possible to quantitatively assess the concentration of miR-16-5p on each cell line. Together, these two complementary MS-based strategies establish a platform for the quantitative evaluation of nanocarrier-mediated miRNA targeting, offering new avenues for the development of miRNA-based cancer therapeutics.