PpAtg9 is essential for the selective degradation of peroxisomes (e.g., pexophagy) in Pichia pastoris. This integral membrane protein is synthesized in the endoplasmic reticulum (ER) and transported to a unique peripheral compartment (Atg9-PC). A putative ER exit motif has been identified and when deleted results in the accumulation of PpAtg9 within the ER. Upon the onset of micropexophagy, PpAtg9 transits from the Atg9-PC to perivacuolar structures (PVS) and sequestering membranes (SM) that arise from the vacuole to engulf the peroxisomes. In this article, we will discuss the transport pathways of PpAtg9 and those factors responsible for its trafficking.