Fluorescence and surface-enhanced Raman scattering (SERS) spectroscopy were employed to investigate the cellular uptake of rhodamine 6G (R6G) alone and of R6G loaded with gold nanoparticles (AuNPs) by endothelial cells. R6G plays the role of a Raman reporter in SERS but also displays strong fluorescence. The presence of bare R6G molecules and R6G-AuNPs in the cytoplasm of the cells is detected via the 2D fluorescence of the dye after a 0.5 h of the incubation with R6G and R6G-AuNPs, and then the concentration of the dye increases within 4 h of exposure. The examination of the cellular uptake of the R6G and R6G-AuNPs species at different temperatures suggests that the internalization of the R6G-AuNPs into endothelial cells occurs mainly via endocytosis. 3D fluorescence imaging of R6G inside cells reveals inhomogeneous distribution of the dye in the cytoplasm. The SERS signal of the Raman reporter inside the cell disappears after 2 h of incubation with R6G-AuNPs and then amino acid residues, purines and pyrimidines become SERS-active via their interactions with the gold. The results highlight the significance of using multiple techniques to cover a spectrum of issues in the application of SERS nanosensors for probing an intracellular environment under comparable and standardized conditions.