Middle-aged women belong to a risk group for metabolic dysregulation and menopausal symptoms, mainly due to a dramatic hormonal shift. Supplementation with functional compounds or a single nutrient has been dominantly explored as a nutritional approach for improving aging-related health parameters. However, a meal-based approach might be another strategy for promoting the overall health of the target population. This pilot study aimed to develop a meal-based intervention for middle-aged women and to evaluate its potential health benefits. Considering the nutrient intake status of Korean middle-aged women, diets enriched with four major nutrients (isoflavone, omega-3, fiber, and calcium) were designed and provided to forty-nine women aged 50 to 65 with mild levels of menopausal symptoms for 8 weeks. In the post-intervention phase, they showed reduced body weight and body fat, and improved biochemical metabolic parameters with decreased levels of cholesterol, low-density lipoprotein-cholesterol, ApoB, and fasting insulin. Moreover, bone resorption markers and menopause symptoms were lower in the post-intervention phase. In conclusion, the meal-based intervention might be a prominent strategy for overall health promotion in relatively healthy middle-aged women and further investigation is needed to test its efficacy with a randomized controlled study.