The increase in antioxidant defenses mediated by physical exercise signaling is proposed to be a protective factor against brain aging and neurodegeneration. However, the processes involved, particularly the response of senescence markers and cell fitness status in the context of Alzheimer’s disease (AD) pathology, remain unclear. We analyzed male and female 5XFAD transgenic AD mice subjected to 6 months of voluntary wheel running using molecular and behavioral techniques. Levels of mRNA of selected genes, mitochondrial complex proteins, and proteasomal function, were analyzed in the cerebral cortex or hippocampus. In an exploratory translational approach, proteasomal dynamics- and senescence-related genes were analyzed in peripheral blood from middle-aged amateur sportsmen. Physical exercise increased expression of antioxidant genes and modulated epigenetic genes in 5XFAD male and female mice. An increase in protein levels of hippocampal mitochondrial complexes CIII and CV was also induced in males. Both exercised 5XFAD mice and veteran sportsmen showed improved proteasomal status and decreased expression of senescence genes. Exercised mice showed memory and behavior preservation, as well as increases in brain metabolic fitness and gene modulation. These changes may contribute to the neuroprotective effect of physical exercise.