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Background  The ewe lamb nutritional and physiological state interfere with the ovarian environment and fertility. The lack or excess of circulating nutrients reaching the ovary can change its gene expression. A protein deficiency in the blood caused by an  Haemonchus contortus  abomasal infection is detrimental to the organism’s development during puberty. The peripubertal period is a time of intensive growth that requires a high level of nutrients. An essential feature controlling pubertal arousal and female reproductive potential is ovarian follicle growth activation. Protein supplementation improves the sheep’s immune response to helminthic infections. We aimed to determine if supplementing protein in infected ewe lambs’ diet would impact the ovarian environment leading to earlier ovarian follicle activation than in infected not supplemented animals.    Methods  We fed 18 Santa Ines ewe lambs ( Ovis aries ) - bred by the same ram - with either 12% protein (Control groups) or 19% protein (Supplemented groups) in their diets. After 35 days of the diet, they were each artificially infected or not with 10,000  Haemonchus contortus  L3 larvae. Following 77 days of the diet and 42 days of infection, we surgically collected their left ovaries and examined their genes expression through RNA sequencing.    Results  We found that protein supplementation in infected animals led to an up-regulation of genes (FDR  p -values < 0.05) and biological processes (p-value cut-off = 0.01) linked to meiotic activation in pre-ovulatory follicles and primordial follicle activation, among others. The supplemented not infected animals also up-regulated genes and processes linked to meiosis and others, such as circadian behaviour. The not supplemented animals had these same processes down-regulated while up-regulated processes related to tissue morphogenesis, inflammation and immune response.    Conclusion  Diet’s protein supplementation of peripubertal infected animals allowed them to express genes related to a more mature ovarian follicle stage than their half-sisters that were not supplemented. These results could be modelling potential effects of the interaction between environmental factors, nutrition and infection on reproductive health. When ovarian activation is achieved in a timely fashion, the ewe may generate more lambs during its reproductive life, increasing sheep breeders’ productivity.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12917-021-03020-7.

Ovarian activation delays in peripubertal ewe lambs infected with Haemonchus contortus can be avoided by supplementing protein in their diets