7-Nitrobenz-2-oxa-1,3-diazole (NBD) is a widely used fluorescent label for proteins, peptides, and lipids. Its chloride derivative, NBD-Cl, can be highly reactive toward thiol and amine groups, forming stable fluorescent adducts. When labeling the ubiquitous lipid molecule ceramide, NBD-ceramide (NBDCER) aids in visualizing sphingolipid metabolism in cells. This study investigates intracellular molecular changes induced by NBD-Cl and NBDCER using surface-enhanced Raman scattering (SERS). SERS spectra from the endolysosomal compartment of two cell lines, 3T3 fibroblast cells and J774 macrophage cells, obtained with gold nanoparticles as probes, reveal changes in the molecular composition and interactions under different incubation conditions. Applying the random forest (RF)-based algorithm surrogate minimal depth (SMD) to the SERS data to identify important spectral classifiers and their relations, both NBD-Cl and NBDCER are found to alter the biochemical makeup of the endolysosomal compartment. The data indicate significant structural and interaction changes in the molecular constituents of the cells that are in agreement with possible interference of the labels in the cellular metabolism and the reaction of NBD-Cl with functional groups of cellular molecules.