Enzymatic hydroesterification is a heterogeneous catalyzed process suitable for the conversion of low-cost feedstocks in biodiesel production, namely, because of its tolerance to high free fatty acid contents. The current study describes the use of Fourier transform infrared spectroscopy (FTIR) to monitor biodiesel production using enzymatic hydroesterification and, as raw materials, acid oil from soapstock and olive pomace oil. Acid oil (~34 wt.% FFA) and olive pomace oil (~50 wt.% FFA) were first hydrolyzed (35 °C, 24 h, 200 rpm, 3 wt.% of lipase from Thermomyces lanuginosus, and 1:0.5 water:oil ratio, w:w), and then enzymatic esterification was performed (35 °C, 7 h, 200 rpm, 2 wt.% of lipase from Thermomyces lanuginosus, and 2:1 molar ratio of methanol to acid). FTIR analyses were conducted on the products using a Jasco FT/IR-4100 with a scanning range of 4000–650 cm−1 at 4 cm−1 spectral resolution and 54 scans. For free fatty acid (FFA) quantification, the C=O band at 1708 cm–1 was used, corresponding to the carboxylic acid, whereas for fatty acid methyl ester (FAME) quantification, the peak corresponding to C=O at 1746 cm−1 was considered, which corresponded to the ester. The results were calibrated using volumetric titration and gas chromatography analyses, concerning FFA and FAME quantification, respectively. The best conditions for analysis were determined, and a calibration method was established. FTIR has shown to be a simple, fast, and clean technique suitable to monitor hydroesterification of low-cost feedstocks.