The aim of the present study was to examine whether a holistic approach combining nutrition and lifestyle counselling with the consumption of milk and yoghurt enriched with calcium, vitamin D(3) and phylloquinone (vitamin K(1)) or menaquinone (vitamin K(2)) would have any additional benefit on bone mineral density (BMD) indices measured at various skeletal sites using two different techniques, dual energy X-ray absorptiometry and quantitative ultrasonography (QUS). A sample of 115 postmenopausal women were randomized to three intervention groups, receiving daily via fortified milk and yoghurt and for 12 months, 800 mg calcium and 10 μg vitamin D(3) (CaD group, n = 26); 800 mg calcium, 10 μg vitamin D(3) and 100 μg vitamin K(1) (CaDK1 group, n = 26); 800 mg calcium, 10 μg vitamin D(3) and 100 μg vitamin K(2) (CaDK2 group, n = 24); and a control group (CO group, n = 39) following their usual diet. All three intervention groups attended biweekly nutrition and lifestyle counselling sessions. Total BMD significantly increased in all three intervention groups and these changes were significantly higher compared to the CO (P < 0.001). Furthermore, the significant increases observed for L2-L4 BMD in the CaDK1 and CaDK2 groups were found to be significantly higher compared to the decrease observed in the CO (P = 0.001). No significant differences were observed for QUS parameters. The combined approach used in the current study led to favourable changes for all three intervention groups in total body BMD, while an additional benefit was observed for L2-L4 BMD in CaDK1 and CaDK2 groups. No significant differences were observed among groups in any of the QUS parameters.