We demonstrate a continuous reactor for performing the ozonolysis of fatty acid methyl esters (FAMEs) using liquid CO2 as solvent. The fast reaction kinetics allows the use of small-volume reactors to completely convert the FAMEs, forming secondary ozonides as the primary products. The short residence times also help maximize the yields of the secondary ozonides by minimizing over-oxidation and the formation of oligomeric products. The liquid CO2 medium promotes safe reactor operation by providing an essential fraction of overall reactor cooling and by diluting the vapor phase organics. We also demonstrate a continuous stirred reactor for the safe thermal decomposition of the secondary ozonides to their corresponding acids and aldehydes. Using a lumped kinetic model for the thermal decomposition of the ozonolysis products, we estimate activation energy values of 108.6 +/- 0.6 kJ mol(-1) for the decomposition of secondary ozonides and 122 +/- 3 kJ mol(-1) for the decomposition of the undesired oligomeric species. (c) 2017 American Institute of Chemical Engineers AIChE J, 63: 2819-2826, 2017