The production of bio-fuels as a substitute for crude oil is steadily increasing. The reactions producing bio-fuels need detailed analysis concerning mechanism and reaction kinetics to increase yield. Standard analytical methods provide a way to monitor the reaction in real-time but detailing the mechanism through chemical shift fingerprinting is not possible using these methods. The reaction kinetics during biofuel production can be followed in real-time by nuclear magnetic resonance (NMR) spectroscopy by passing reaction mixture through the magnet. The present work reports the use of desktop NMR spectroscopy for a real-time study of the transesterification of triglycerides (vegetable oil) with methanol for formation of methyl esters (biodiesel) to detail catalytic activity, reaction mechanism and kinetics. The reaction was investigated for different catalyst concentrations, different molar ratios of reactants, and different temperatures. The changes in the chemical shift of the hydroxyl protons in the reaction mixture resulting from changing catalyst concentration and temperature provide information about the role of the catalyst in the aqueous and organic phases. The reaction was determined to be mass transfer controlled in the initial stage and kinetically controlled at later stage depending upon the reaction conditions. Analysis of the reaction for different molar ratios of oil and biodiesel and for increasing methanol concentration suggests the formation of dimers. The time variation of the methyl ester (biodiesel) concentration was determined by partial least squares regression (PLS-R) using high-field NMR spectroscopy as reference. To obtain rate constants for each reaction the kinetics were modeled assuming fatty acid methyl esters as major product, and mono and diglycerides as intermediates. The 95% confidence intervals were derived by a Monte-Carlo analysis. The reaction kinetics are compared to those obtained by peak fitting of low-field spectra.