Heat stress (HS) affects spermatogenesis and sperm maturation, decreasing sperm quality. Yet sperm morpho-functional changes caused by HS in Nellore bulls are not fully elucidated. This study aimed to show the chronological effects on sperm quality of HS during spermatogenesis and sperm maturation until recovery of the seminiferous epithelium in Nellore bulls. Nine Nellore bulls were distributed into control and heat stress (HS-scrotal bags/96 h) groups. The study was divided into five Periods: 1. Control (14-7 days before HS); 2. Stored sperm (0–7 days after HS); 3. Sperm maturation and late spermatogenesis (14–42 days after HS); 4. Early spermatogenesis (49–63 days after HS), and 5. Recovery (70–77 days after HS). Semen was collected once a week and evaluated for sperm motility, morphology, plasma, acrosome, and mitochondrial membranes, lipid peroxidation, and DNA fragmentation. Sperm characteristics were similar between groups in Periods 1 (control). During Period 2, HS increased detached normal head defect and decreased mitochondrial membrane potential, denoting effects on the sperm stored at the epididymis cauda. In Period 3, HS decreased sperm motility, plasma membrane integrity, and mitochondrial membrane potential and increased abnormal sperm, lipid peroxidation, and DNA fragmentation; reflecting the effects on sperm that were in the epididymis body and head and late spermatogenesis (spermiogenesis and meiosis). In Period 4, HS maintained a reduction in the mitochondrial membrane potential and an increase in abnormal sperm; injuries that could occur during early spermatogenesis (mitosis). Finally, in Period 5, the groups were similar, confirming the recovery of the seminiferous epithelium after HS. This study provides insights on the effects of HS on the complete process of sperm maturation and spermatogenesis, until recovery in sperm from Nellore bulls.