Peroxisomes are critical organelles, housing various essential processes conserved across multicellular organisms. Most notable reactions include fatty-acid -oxidation and the detoxification of reactive oxygen species generated as byproducts from diverse oxidative reactions. Peroxisomes also house specialized processes depending on the organism, tissue, and developmental age, such as phytohormone production in plants. Peroxins, or PEX proteins orchestrate the biogenesis and maintenance of these organelles. Despite the evidence for tunability and dynamic changes in peroxisome numbers and function during development and environmental challenges, our understanding of how this organelle is regulated remains limited. Autophagy is a cellular system that targets components of the cell for degradation in the vacuole (of plants or yeast) or the lysosome (of animals). Autophagy can be selective, and the degradation of peroxisomes through this process is called pexophagy. By comparing protein accumulation in various peroxin mutants to accumulation in both wild type and seedlings incapable of autophagy (atg mutants), I found that pex2, pex4, pex10, and pex14 mutants stabilized several peroxisomal proteins similarly to atg mutants in darkness conditions. I also examined autophagy and pexophagy induction using immunoblotting to detect cleavage of autophagy and pexophagy reporters in a variety of conditions. I found that pexophagy occurs during development but is not robustly induced in many autophagy-inducing conditions. Finally, I explored the connection between darkness-induced autophagy and carbon starvation and found that darkness induces autophagy even when fixed carbon is exogenously supplied. My investigations implicate several peroxins in pexophagy modulation and demonstrate that the environmental conditions regulating pexophagy are complex and distinct from the triggers of general autophagy. As future work characterizes subpopulations of peroxisomes within Arabidopsis, the assays described herein provide a foundation for the further elucidation of when, where, and how pexophagy occurs in plants.