Spermatogenesis prompts a series of striking changes in the intracellular composition and the spatial arrangement of organelles. Among those changes include alterations in the morphology of mitochondria. This study showed that condensed mitochondria are distinct organelles with a stable ultrastructure and a distinguishable proteome. To investigate the development of condensed mitochondria, they used proteomic analysis, respirometry, and electron microscopy with tomography. This dataset contains proteomic and imaging data. The results indicate that condensed mitochondria are formed from orthodox mitochondria by extensive transformations to support the formation of the acrosomal matrix.