Fusarium fujikuroi is an industrial producer of gibberellic acid (GA3), a phytohormone of agricultural interest. Despite the high concentration of nutrients used for its production, GA3 yields remain low, highlighting the importance of identifying the major metabolites synthesized during GA3 synthesis. Therefore, the principal aim of this work was to evaluate organic acid production during F. fujikuroi batch cultures by determining GA3 production and organic acid profiles using Fourier transform infrared spectroscopy (FTIR) and liquid chromatography (HPLC) analysis. Significant differences in compound quantification were found; five organic acids, namely lactic, malic, citric, succinic and maleic, were detected by HPLC (in g/L: 101.09, 10.66, 2.80, 6.94 and 1.07, respectively). In addition, eight organic acids were determined by FTIR, namely lactic, butyric, pyruvic, fumaric, malic, succinic, maleic and oxalic (in g/L: 62.97, 19.19, 11.92, 7.54, 2.30, 4.36, 1.25 and 1.06 g/L, respectively). GA3 production was also quantified, reaching nearly 5.0 g/L as determined by HPLC and UV-Vis, and FTIR yielded 2.20 g/L. This report found that the low yields obtained in GA3 production are related to the side conversion of raw materials into organic acids as byproducts. In addition, the FTIR technique can be employed as an innovative strategy for the quantification of metabolites to provide relevant information on F. fujikuroi metabolic regulation. This enables the spread of its application as a biotechnological tool in high-value-added processes with potential for industrial-scale GA3 production.