The initial aim of the paper is to dramatically improve the pretreatment stage of biodiesel production, which converts problematic free fatty acids to fatty acid methyl esters, by introduction of a microbubble mediated reactive distillation stage instead of acid pretreatment. This will shift the conventional esterification process towards completion with a yield higher than 80%, even without high excess methanol. Application of ozone microbubbles has the advantage over acid gas catalysis in that it gives higher conversion and leaves no catalyst residue and requires no further catalyst recovery separation steps (a “phantom” catalyst). Unreacted ozone breaks down into oxygen, so the off-gases are just a humid air stream that can be vented. Importantly, ozonolysis breaks carbon–carbon double bonds into aldehydes and carboxylic acids. Many ester species were found after contacting the feedstock with ozone-rich microbubbles, depending on the molecular structure of the alcohols for the ozonolysis of oleic acid with alcohols, i.e., methanol, ethanol, n-propanol, iso-propanol, and n-butanol. In the case of ozonolysis of used cooking oil mixed with methanol, the results from the GC–MS show that all saturated free fatty acids (including palmitic acid, stearic acid, and myristic acid) are converted to methyl esters within 20 h of 60 °C ozonolysis, whereas trace amounts of these chemicals remain at lower temperatures. The results also show that the conversion of oleic acid to form oleic acid methyl ester is 91.16% after 32 h of ozonolysis at 60 °C. Therefore, the free fatty acid content in used cooking oil is less than 1.33%, which makes it suitable as a reactant for biodiesel production via transesterification. However, this result is different from the result provided by ASTM D974 in that the acid numbers decrease dramatically by 25% at the beginning of ozonolysis followed by a plateau. Moreover, if the fluidic oscillator is used to generate bubbles in ozonolysis of oleic acid mixed with methanol, the results show that the yields of ozonolysis product 1-nonanal increase by 30%. This observation means that ozonolysis of oleic acid is relative to the specific interfacial area, and favoured at low liquid temperatures.