The sesquiterpenes (+)-germacrene A and (-)-germacrene D are natural semiochemicals currently employed in developing alternative and more sustainable crops. In planta (or in Nature), these relatively complex cyclodecadienes C15 hydrocarbons are biosynthesised from farnesyl diphosphate (FDP) by the action of sesquiterpene synthases GAS and GDS. On the expectation that modifications of their chemical structure could lead to compounds with enhanced biological properties, a small library of alkyl- and fluorine-modified germacrene A and D analogues were synthesised upon exposure of the corresponding FDP analogues to (+)-germacrene A or (-)-germacrene D synthases from Solidago Canadensis. Two novel incubation procedures were developed to secure the production of these valuable germacrenes in sufficient amounts for NMR characterisation as well as for their in vivo evaluation against aphids. While the use of deuterated extracting solvents in batch experiments was essential to characterise the enzymatic products and monitor their relative stability, the production of these novel bioactive semiochemicals was substantially boosted through the use of modern continuous flow extraction techniques. In addition, the synthesis and enzymatic evaluation of two hydroxylated FDP analogues as mechanistic probes provided evidence in support of a 1,10-cyclisation reaction under (+)-B-cadinene synthase catalysis. Results obtained from the in vivo evaluation of novel analogues of (+)-germacrene A or (-)-germacrene D can be used in the future for designing agrochemicals with enhanced repellent activity for pest control. Further optimisation of flow chemoenzymatic preparation of sesquiterpenes could be performed, perhaps by including immobilised enzymes with improved stability in the design of the flow reactor. The potential of hydroxyl FDP analogues for exploring terpene synthases mechanism is yet to be evaluated.