Mitophagy, the autophagy of mitochondria, is thought to be an essential quality control (QC) mechanism of pathophysiological relevance in mammals, with dysfunctional mitophagy being implicated diseases such as Parkinson’s, cancer and ageing. However, if and how mitophagy proceeds within specific cellular subtypes in vivo has remained unclear, largely due to a lack of tractable tools and models. To address this, we developed “mito-QC”, a transgenic mouse with a pH-sensitive fluorescent mitochondrial signal. This allows the assessment of mitophagy and mitochondrial architecture in vivo. mito-QC revealed that mitophagy is a significant process in most tissues, even under basal conditions. However, within tissues it can be spatially restricted to distinct cell types, particularly those with high metabolic demands such as dopaminergic neurons in the brain, proximal tubule cells in the kidney, or cardiomyocytes within the heart. The reporter also revealed the striking differences between mitochondrial morphology in different tissue cell types and enabled easy visualization of the mitochondrial reticulum in skeletal muscle. Thus mitophagy displays a pervasive nature under basal conditions, yet how this changes under physiological stimuli and stress, such as during exercise, remains to be determined – as does the consequences of this process. We hope that mito-QC will be a powerful tool in this endeavour.