Heat stress (HS) is a significant environmental factor that leads to substantial financial losses in the rabbit industry. In the present study, betalains and organic selenium (Ose) were used as natural protection against HS to improve rabbits' reproductive and health status. Forty-five three-month-old V-line male rabbits were distributed into three groups, each consisting of 15 rabbits with the same average weight. The first group, acting as the control group, received a basal diet without any treatment, while the second and third groups administered betalains (1.4 g betalains/kg diet) and Ose (0.7 g OSe/kg diet), respectively. In terms of semen quality, the malondialdehyde (MDA), superoxide dismutase (SOD), glutathione content (GSH), and adenosine triphosphate (ATP) were significantly improved by using betalains and Ose. Betalains and Ose increased the sperm motility, motility index, sperm normality, and livability. Furthermore, both treatments significantly increased the levels of testosterone, luteinizing hormone (LH), follicle-stimulating hormone (FSH), 5-hydroxytryptamine (5-HT), and dopamine compared to the control group. In the betalains and Ose -treated groups, there was upregulation in the growth-related genes and glutathione peroxidase (GPX) in the liver and caecum. Conversely, the betalains and Ose -treated groups exhibited downregulation of tumor necrosis factor (TNF) and fas cell surface death receptor (FAS) in the liver and caecum compared to the control. The study's findings revealed that betalains and Ose were useful for improving the reproductive and health status of rabbits subjected to HS.