Hormonal treatments used in the artificial insemination (AI) of sheep can cause several physiological problems that can affect negatively fertility and animal health; however, AI protocols based on the detection of natural estrus offer a more sustainable option and can achieve high fertility. In this study, an AI protocol at natural estrus in organic Churra sheep was performed. In the first phase (AI protocol development), 125 ewes were exocervically inseminated, and their fertility was assessed based on the following factors: number of AI, physiological state, body condition, estrus detection–AI interval, and vaginal fluids in cervix. That protocol was repeated for six consecutive years. In all individuals, fertilities based on the timing of insemination after estrus detection were very high. Lactating ewes produced better results than did dry ewes, which was probably because of the better feeding of the former. In addition, double insemination increased the fertility of ewes whose estrus was detected within 16 h of onset. Body condition and amount of vaginal fluid were correlated with fertility. Exocervical inseminations at natural estrus can produce acceptable fertility and prolificity in Churra ewes.