Nitrogen availability is key factor for plant metabolism and has a strong impact on the biosynthesis of secondary plant metabolites. A number of these metabolites are involved in the response to stress. In this paper, we investigated the effect of different N conditions in leaves of Lotus corniculatus. Low nitrogen conditions strongly enhanced the biosynthesis of phenolic compounds in leaves, inducing the expression genes encoding for key enzymes of phenolic metabolism such as phenylalanine ammonia lyase, chalcone synthase and isoflavone synthase. Kaempferol and quercetin glycosides as well as isoflavanes accumulated in leaves. Surprisingly, if the nitrogen availability was limited, but without nitrogen deprivation symptoms, an increase in the levels of phenylpropane acids and a decrease in the levels of kaempferol glycosides was detected. Especially the decrease in malonylated kaempferol derivatives and the kaempferol glycosides substituted by rhamnose in the 3-O position. The L. corniculatus malonyltransferase 1 gene is likely involved in the malonylation of the kaempferol glycosides.