Caloric restriction (CR) studies have traditionally focused on species with conventional reproductive roles, emphasizing female’s greater investment in costly gametes and parental care. The divergent impact of CR on males and females is evident across species, the factors driving this variation, i.e., resource allocation in reproductive elements vs. distinct life histories remain unclear. To address this, we investigated the effects of CR on growth, gene expression, and intestinal microbiota in the lined seahorse Hippocampus erectus, a species with male pregnancy and unique life history. Juvenile seahorses were subjected to ad libitum (AL) or CR for 5 months. CR stunted male (but not female) growth and brood pouch development, reflecting the energy demands associated with pouch development and parental care. Transcriptome analysis demonstrated organ- and sex-specific responses to CR with distinct lipid and energy-related pathways activated in male and female livers, indicative of survival enhancement strategies. Fasting had minimal impact on spermatogenesis, but downregulated lipid metabolic and inflammatory genes in ovaries, emphasizing the importance of pre-copulatory resource allocation in female gametes. While microbial diversity increased with fasting, no discernible sex-specific effect on hind-gut microbiota was identified. Our research indicates that nutrient limitation´s impact on males and females is influenced by their allocation of resources to reproduction and parental investment, rather than being solely determined by biological sex. We underscore the significance of studying species with diverse reproductive strategies, sex roles, mating systems, and life-history strategies to understand the sex-specific effects of caloric restriction.