Our aim is to analyse the effect on bone mass of: (1) physical fitness performance on a specific group of physical activity (PA) and, (2) PA on a specific physical fitness performance group. Bone mineral content (BMC) by dual energy X-ray absorptiometry (DXA) and PA by accelerometers was assessed in 373 Spanish adolescents (182 males). Adolescents were classified as: active and non-active (≥60 or <60 min day(-1) of moderate-vigorous PA). Fitness was assessed through speed/agility, strength and cardiorespiratory tests. Adolescents were classified by tertiles (T1, T2 and T3). ANCOVA was used for the analysis with sex, height, lean mass, calcium intake and pubertal status as covariates. Adolescents with lower strength, speed/agility and cardiorespiratory fitness (CRF) showed lower BMC in the whole body and extremities compared with adolescents with better results in these tests, mainly those non-active adolescents. Non-active adolescents with high fitness levels showed higher BMC (whole body and upper limbs) than active ones. The conclusions included: (1) within the non-active group, lower levels of fitness were associated with lower BMC; this might be through PA or trough an effect of PA on muscle mass. (2) Non-active adolescents with high level of fitness in most fitness tests showed higher BMC than their active peers, in spite of their lower PA levels. These unexpected results could be influenced by several factors such as genetics, nutrition, type of exercise or sport, hormones and skeletal age.