Here, we show that the loss of YME1L in the nervous system impairs mitochondrial morphology and proteostasis throughout the nervous system but results in striking cell‐type‐specific neurological defects in mice: While newborn mice show microphthalmia with retinal inflammation and cataracts, spinal cord axons of the dorso‐lateral column progressively degenerate with age, impairing coordinated movements. This evidence concerns the gene YME1L1 and microphthalmia.