Plant cell suspension culture of T. peruviana is a feasible biotechnological platform for the production of secondary metabolites with anti-proliferative/cytotoxic activity, as phenolic compounds (PC); however, different in in vitro growth conditions may affect the production, demanding strategies to increase the metabolite biosynthesis, as well as the development of sensitive and rapid analytical methods for metabolite monitoring. The Fourier transform near-infrared (FT-NIR) spectroscopy and Reversed-phase high-performance liquid chromatography (RP-HPLC) combined with Multivariate analysis (MVA) were used to detect significant differences in the PC production in cultures treated with two elicitors. The results suggest that the FT-NIR-MVA is useful for discriminating samples according to the treatment, showed significant influence of the PC signal. RP-HPLC-MVA showed that the elicitor effect occurs at 72 h post-elicitation. Detection of dihydroquercetin (maximum concentration = 12.59 mg/L), a flavonoid with anti-cancer properties, is highlighted. Future studies will be aimed at scaling this culture to increase the productivity of dihydroquercetin.