Peroxisomes are small, membrane-bound organelles with a diameter 100–300 nm, which play a pivotal role in many metabolic functions and immunity. Loss of peroxisomal protein function leads to severe metabolic diseases in humans. However, due to their small size, the direct study of peroxisomes in cells requires special experimental approaches. We here applied super-resolution microscopy such as Airy-scan, STED, STORM, and MINFLUX microscopy, to study the peroxisomal morphology, dynamics, and the distribution of peroxisomal proteins in the organelle. Combined with dedicated image analysis and correlation of results from the different techniques, we defined parameters to identify different peroxisomal phenotypes. With this, we highlight consistencies between microscope approaches, variations in phenotypes between different peroxisomal proteins and morphological dependencies on the labelling strategy.