This study investigates the mechanism by which lysosomes drive the selective removal of damaged mitochondrial inner membrane (IMM) sections. Using super-resolution microscopy, the authors discovered that cytosolic IMM-derived vesicles (VDIMs) form during the resting state. These vesicles, devoid of the outer mitochondrial membrane or mitochondrial matrix, are formed when IMM herniates through pores in the outer mitochondrial membrane (OMM) created by the voltage-dependent anion channel (VDAC1). Live-cell imaging revealed that lysosomes engulf these herniating IMM sections, leading to their degradation via a microautophagy-like process. The formation of VDIMs was enhanced in mitochondria undergoing oxidative stress, suggesting their role in maintaining mitochondrial function. The study also found that VDIM formation required calcium release by the OMM-localized voltage-gated anion channel (VDAC) and the lysosomal Ca2+ channel TRPML1. Additionally, the ESCRT machinery was involved in the membrane scission necessary for VDIM formation. Overall, the findings reveal a novel pathway of intramitochondrial quality control, where lysosomal communication and microautophagy-like processes selectively remove damaged IMM sections, protecting the rest of the organelle.This study investigates the mechanism by which lysosomes drive the selective removal of damaged mitochondrial inner membrane (IMM) sections. Using super-resolution microscopy, the authors discovered that cytosolic IMM-derived vesicles (VDIMs) form during the resting state. These vesicles, devoid of the outer mitochondrial membrane or mitochondrial matrix, are formed when IMM herniates through pores in the outer mitochondrial membrane (OMM) created by the voltage-dependent anion channel (VDAC1). Live-cell imaging revealed that lysosomes engulf these herniating IMM sections, leading to their degradation via a microautophagy-like process. The formation of VDIMs was enhanced in mitochondria undergoing oxidative stress, suggesting their role in maintaining mitochondrial function. The study also found that VDIM formation required calcium release by the OMM-localized voltage-gated anion channel (VDAC) and the lysosomal Ca2+ channel TRPML1. Additionally, the ESCRT machinery was involved in the membrane scission necessary for VDIM formation. Overall, the findings reveal a novel pathway of intramitochondrial quality control, where lysosomal communication and microautophagy-like processes selectively remove damaged IMM sections, protecting the rest of the organelle.