There is an unmet need for interventions with better compliance that prevent the adverse effects of sex steroid deficiency on the musculoskeletal system. We identified a blueberry cultivar (Montgomerym [Mont]) that added to the diet protects female mice from musculoskeletal loss and body weight changes induced by ovariectomy. Mont, but not other blueberries, increased the endogenous antioxidant response by bypassing the traditional antioxidant transcription factor Nrf2 and without activating estrogen receptor canonical signaling. Remarkably, Mont did not protect the male skeleton from androgen‐induced bone loss. Moreover, Mont increased the variety of bacterial communities in the gut microbiome (α‐diversity) more in female than in male mice;​ shifted the phylogenetic relatedness of bacterial communities (β‐diversity) further in females than males;​ and increased the prevalence of the taxon Ruminococcus1 in females but not males. Therefore, this nonpharmacologic intervention (i) protects from estrogen but not androgen deficiency;​ (ii) preserves bone, skeletal muscle, and body composition;​ (iii) elicits antioxidant defense responses independently of classical antioxidant/estrogenic signaling;​ and (iv) increases gut microbiome diversity toward a healthier signature. These findings highlight the impact of nutrition on musculoskeletal and gut microbiome homeostasis and support the precision medicine principle of tailoring dietary interventions to patient individualities, like sex.