Surface-enhanced Raman scattering (SERS)-encoded nanoparticles are used for bioimaging, on account of their well-defined Raman spectra and biocompatibility, which allow long incubation times with high signal stability and no cytotoxicity. However, reliable analysis of SERS bioimaging requires quantification of the amount of encoded nanoparticles that have been taken up by cells and the effect of subsequent dilution due to cellular division (mitosis). Although methods such as elemental analysis and flow cytometry can be used to quantify nanoparticle uptake, these are both end-point measurements in which a cell population is screened rather than looking at individual cells. In contrast, SERS imaging can be applied at multiple timepoints to the same individual cells without damaging the biological sample. We present the application of both supervised and unsupervised multivariate analyses, to quantify the intracellular amount of SERS tags in individual MCF7 living cells, toward the characterization of cellular uptake in vitro. The obtained results from both methodologies were validated by standard elemental analysis techniques.