Post-menopausal conditions exacerbate the biological aging process and this is often accompanied by visceral adiposity with sarcopenia. Mitochondrial impairment is a hallmark of frailty and sarcopenia in the elderly. However, the exact mechanism underlying the development of obesogenic sarcopenia and the involvement of mitochondria remains unclear. This study confirmed that there is a decline in muscle mass and function as well as mitochondrial dysfunction in the quadriceps of ovariectomized (OVX) mice. To investigate the role of microRNA (miRNA) in this process, we performed miRNA and mRNA arrays and found that miR-141-3p directly targets and downregulates FK506 binding protein 5 (Fkbp5) and Fibin. Overexpression of miR-141-3p decreased mitochondrial function and inhibited myogenic differentiation in C2C12 cells. These effects were mediated by Fkbp5 and Fibin inhibition. Conversely, knockdown of miR-141-3p increased mitochondrial respiration and enhanced myogenesis. Treatment with β-estradiol effectively reversed the palmitic acid-induced upregulation of miR-141-3p and subsequent downregulation of Fkbp5 and Fibin. In conclusion, miR-141-3p is upregulated in OVX mice, and this is associated with mitochondrial dysfunction through inhibition of Fkbp5 and Fibin. These findings suggest that inhibiting miR-141-3p could be a therapeutic target for alleviating obesogenic sarcopenia.