Ethnopharmacological relevanceTongkat Ali (Eurycoma longifolia Jack) is a chief herbal medicine that is well recognized for its aphrodisiac properties, available in various commercial products worldwide. Aim of the studyThe aim of this work is to identify the different classes of secondary metabolites present in Tongkat Ali commercial products versus authenticated root, and to assess its root extract mitigative effect against 5-flurouracil (5FU)-induced testicular toxicity. Materials and methodsHigh-resolution UHPLC-QTOF-MS/MS metabolites analysis was utilized on the ethanolic Tongkat Ali extract (TAE) parallel to three Mlayasian commercial products, followed by a multivariate data analysis to understand the variability among UHPLC-MS metabolites datasets. Adult male rats were treated with 5-Fluorouracil (5FU) ± Tongkat Ali extract. Semen parameters, serum testosterone, LH, and FSH, and testicular oxidative stress biomarkers like malondialdehyde (MDA) levels, Nuclear factor kappa B (NF-κB) and erythroid 2–related factor 2 (Nrf2) were analyzed. ResultsThe main categories of secondary metabolites identified through UHPLC-MS/MS profiling were quassinoids, alkaloids, fatty acids, lignans and coumarins. Long Jack Plus® ELP-2 clustered alongside authentic roots ELR on the negative side, while Naturelle® ELP-1 and Nu-Prep-LEAKI® ELP-3 were positioned on the opposite side. The OPLS-DA model was used to identify markers for preparations from authentic roots, with commercial products enriching in ailanthone epoxide. In vivo results showed that 5FU reduced sperm parameters by 42%, while TAE improved sperm quality by 35–43% and 58–74% at dose of 400 and 800 mg/kg, respectively. Testosterone, reduced by 74% with 5FU, increased 2.3- to 3.2-fold with TAE. TAE also reduced MDA by 31–62%, NF-κB by 32–55% and increased Nrf2 by 1–2 folds. ConclusionThe manuscript presents a comparative metabolomics study and in vivo investigation into the potential of Tongkat Ali root to improve testicular function in male rats intoxicated with 5FU, an area not previously explored. Further research is required to understand the mechanisms.