Survival in changing and challenging environments requires an organism to efficiently obtain and use its resources. Due to their sessile nature, it is particularly critical for plants to dynamically optimize their metabolism. In plant primary metabolism, metabolic fine-tuning involves feed-back mechanisms whereby the output of a pathway controls its input to generate a precise and robust response to environmental changes. By contrast, few studies have addressed the potential for feed-back regulation of secondary metabolism. In Arabidopsis, accumulation of the defense compounds glucosinolates has previously been linked to genetic variation in the glucosinolate biosynthetic gene AOP2. AOP2 expression can increase the transcript levels of two known regulators (MYB28 and MYB29) of the pathway, suggesting that AOP2 plays a role in positive feed-back regulation controlling glucosinolate biosynthesis. We generated mutants affecting AOP2, MYB28/29, or both. Transcriptome analysis of these mutants identified a so far unrecognized link between AOP2 and jasmonic acid (JA) signaling independent of MYB28 and MYB29. Thus, AOP2 is part of a regulatory feed-back loop linking glucosinolate biosynthesis and JA signaling and thereby allows the glucosinolate pathway to influence JA sensitivity. The discovery of this regulatory feed-back loop provides insight into how plants optimize the use of resources for defensive metabolites.