Peroxisomes are important membrane‐bound organelles that are involved in a multitude of metabolic processes. Peroxisomal biogenesis factor 3 (Pex3) is a crucial peroxisomal membrane protein (PMP) that plays a vital role in many of these processes through the specific recruitment of several binding partners. In the yeast Hansenula polymorpha , Pex3 recruits PMP import receptor Pex19, the receptor for newly synthesized PMPs; autophagy‐related protein 30 (Atg30), a protein involved in the selective breakdown of peroxisomes (pexophagy); and inheritance of peroxisomes protein 1 (Inp1), a protein important for peroxisome retention in mother cells. Here, we show that the overexpression of any of these proteins affects peroxisomal processes, with the level of overexpression being the primary determinant of competition. This finding is confirmed by our analysis based on the crystal structure model of the H. polymorpha Pex3–Pex19 complex and AlphaFold2 predictions. It shows that the interaction regions of Pex3 with these proteins overlap. These results provide a crucial insight into the complex role of Pex3 in regulating different processes in peroxisome biology.