The aim of this work was to identify and quantify the metabolites present in the roots of Combretum lanceolatum inoculated with its endophytic fungi. The metabolomics was accomplished using the 1H nuclear magnetic resonance (NMR) spectral data and evaluated via rNMR software and Madison Metabolomics Consortium Database (MMCD). The principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) showed that plants inoculated with Trichoderma spirale (Ts) present differentiation and discrimination over the time as compared to control. Seven days after Ts fungal inoculation, 15 metabolites were identified at different concentrations comparing to the control plants. The plants inoculated with Ts fungus present the metabolites spermidine and pantothenate in higher concentrations and 3-hydroxybutyric acid and β-alanine in lower concentrations as compared to control plants, indicating any response to biotic stress. These metabolites are involved in various plant processes, including secondary metabolites biosynthesis, energy metabolism and self-defense. Therefore, this work demonstrates the diversification of primary metabolites composition influenced by endophytes inoculation.