Plants produce a wide range of molecules called secondary metabolites which include key participants in the interactions of these sessile organisms with their environment. Some of these molecules allow plants to protect themselves against microbial and herbivore attacks or damaging UV irradiation, while others are involved in the attraction of beneficial microorganisms or animals. For these reasons, plants have to integrate the regulation of secondary metabolite biosynthesis pathways with environmental signals but also within the frame of their development in order to produce the right compounds at the right place and at the right time. The activation of the complex metabolic pathways involves specific transcription factors that regulate the coordinate expression of numerous target genes encoding enzymes of the respective biosynthesis pathways. In this paper, recent research developments on the transcription factors that link secondary metabolite biosynthesis to external signals and plant development are reviewed, focusing on the flavonoid and the terpenoid indole alkaloid biosynthesis pathways. Finally, we discuss how a better knowledge of these transcription factors may be important to design effective molecular tools to improve the production of valuable compounds for the plant and for human use.