Microwave-assisted organic synthesis and continuous-flow techniques have been successfully employed for the preparation of conjugated linoleic acids (CLA), compounds with high health beneficial effects. A good production rate of CLA was obtained. A sustainable methodology for the differentiation of both positional and geometrical CLA isomers (diene), based on the analysis by NMR spectroscopy of the resulting Diels–Alder cycloadducts with an appropriate dienophile, was developed.