Plant peroxisomes are organelles housing different key metabolic pathways in the cell such as photorespiration and fatty acid β-oxidation. The metabolism of phytohormones, polyamines and other key signalling molecules such as reactive oxygen and nitrogen species (ROS and RNS) are housed in these organelles. The presence of a complex antioxidant system that may regulate ROS/RNS level makes peroxisomes a key organelle governing its dependent signalling. The evolution of -omics technologies and the existence of mutants with specifically altered ROS metabolism in peroxisomes, have provided us with a large amount of data and genes that could be regulated in plant responses to stress. All these data point to the existence of a specific transcriptomic footprint associated with peroxisomes. Furthermore, advances in microscopy and the implementation of new molecules have allowed us to visualize organelles in vivo and obtain detailed information about the dynamics of these organelles involving changes in their velocity, peroxules formation and proliferation. In this review, we update the latest information about peroxisomal metabolism and signalling, mainly related to ROS/RNS under control and stress conditions and how the different stimuli affect the plasticity and dynamic of the organelles, which can contribute in turn to plant responses to these stimuli.