Plant metabolic gene clusters consist of neighboring genes that are involved in the biosynthesis of secondary or specialized metabolites. The genes within clusters are typically co-regulated, share a common set of chromatin marks, and code for the biosynthesis enzymes of a single metabolic pathway. Here, we describe three essential protocols for the basic analysis of metabolic gene clusters at transcription, histone modification, and metabolite level. The protocols are specified to clusters in the Arabidopsis thaliana genome and are transferable to other plant species.