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The production of secondary metabolites in Trifolium pratense L. suspension culture of the family of legume plants (Fabaceae) is low, and therefore there was an attempt to increase it by elicitation. New synthetic substance, 2-(2-fluoro-6-nitrobenzylsulfanyl)pyridine-4-carbothioamide, was tested as elicitor—a substance that showed the best elicitation effect after 48-hour application of 1 μmol L−1 concentration. Maximum contents of genistin (11.60 mg g−1 DW), daidzein (8.31 mg g−1 DW), and genistein (1.50 mg g−1 DW) were recorded, and the production of these isoflavonoids thus significantly increased, when compared with the control, by 152%, 151%, and 400%. The maximum content of flavonoids (5.78 mg g−1 DW) and the increase in the production by 142%, when compared with the control, were induced by 6-hour application of 100 μmol L−1 concentration. The tested substance showed to be an effective elicitor of phenylpropane metabolism.