Cryopreservation of spermatozoa is of essential importance for artificial insemination and breeding programs in horses. Besides other factors, spermatozoal motility depends on mitochondrial energy metabolism. Based on changes of single mitochondrial functions it has been suggested that mitochondrial damage during cryopreservation could be a major reason for diminished post thaw semen quality. However, it is still unclear to which extent this influences the whole bioenergetic performance of mitochondria and whether this plays a role during routine cryopreservation procedures. Therefore, it was the aim of this study to compare changes in mitochondrial bioenergetics in spermatozoa during shock freezing and routine cryopreservation. Mitochondrial integrity in spermatozoa was studied by determination of oxygen consumption, mitochondrial membrane potential, and the oxidation of externally added cytochrome c 2+. Shock freezing of spermatozoa resulted in an irreversible loss of mitochondrial functions. However, respiration difference of uncoupled minus resting state and routine respiration also decreased by 48 ± 14 and 58 ± 6% ( p < 0.05), respectively, after routine cryopreservation. This was accompanied by a decline in the mitochondrial membrane potential to 83 ± 4% ( p < 0.05) and spermatozoal motility to 56 ± 11% ( p < 0.05) of prefreezing values. In contrast, the oxidation rates of externally added cytochrome c 2+ by cytochrome c oxidase slightly increased by 26 ± 14% ( p < 0.1) suggesting a partial rupture of cellular and outer mitochondrial membranes. Our data indicate that also widely used cryopreservation protocols for equine spermatozoa need adjustment to optimize post thaw mitochondrial functions.