While mitochondrial degradation via macroautophagy has been extensively characterized, our present study demonstrates that mitochondria can also be selectively eliminated through microautophagy in mammalian cells. We show that Rab32-positive lysosome-related organelles (LROs) in macrophages are sufficiently large to engulf entire organelles, including endosomes and mitochondria. Upon exposure to mitochondrial damage, mitochondria were directly internalized into LROs through a process independent of canonical macroautophagy. Distinct invagination structures were observed under these conditions. This micro-mitophagy mechanism requires Rab32 GTPase activity, phosphatidylinositol 3,5-bisphosphate, ubiquitination, and p62/SQSTM1, but is independent of the ESCRT machinery. Furthermore, we found that mitochondrial clearance via this pathway is critical for macrophage polarization toward the M1 phenotype, which relies on metabolic reprogramming through enhanced glycolysis. Notably, M1 polarization was markedly impaired in Rab32/38 double-knockout macrophages. These findings highlight micro-mitophagy as a previously unrecognized mechanism essential for macrophage function and innate immunity.