Adult-type hypolactasia (ATH) is a clinical syndrome of primary lactase deficiency. A lactose-free diet is advisable to avoid the symptoms linked to the condition, but this potentially creates problems for optimal bone mineralization due to reduced calcium intake. To evaluate the effect of the lactose-free diet on the bone mineral status (BMS), we compared the phalangeal BMS of adolescents with ATH to that of peers on a normal diet. Also, we analyzed the correlations between BMS and dietary behavior, physical exercise, and calcium and vitamin D intake. A total of 102 cases and 102 healthy controls filled out a diet record and underwent phalangeal Quantitative Ultrasound (QUS). No difference in BMS was observed. The time spent on lactose-free diet (4.8 ± 3.1 years) was inversely correlated to the BMS. More than 98% of cases consumed lactose-free milk, but calcium and vitamin D intake were significantly lower. Calcium intake was correlated to physical exercise but not to BMS. Our results suggest that a lactose-free diet does not affect the phalangeal BMS of adolescents with primary lactase deficiency when their diet includes lactose-free cow’s milk. However, there is still a significantly lower calcium intake than in the population reference. The inverse correlation observed between the BMS and the time spent on a lactose-free diet suggests that a long-term follow-up is advisable.