The objective of the present cross-sectional study was to examine the associations of physical activity and the adherence to the Mediterranean dietary pattern (MDP) with bone mineral content (BMC) and density (BMD) in children with overweight and obesity. A total of 177 (n = 80 girls) children with overweight and obesity aged 8 to 12 years old participated in the study. Both BMC and BMD were assessed by Dual-Energy X-ray absorptiometry. Dietary patterns were assessed by the KIDMED questionnaire and two 24-hour recalls. Physical activity was assessed by accelerometers for 7 consecutive days (24 hours/day). Low adherence to the MDP was observed in 82.4% of participants. Higher physical activity levels (of at least moderate intensity) and lower sedentary time were significantly associated with BMC and BMD in children with low adherence to the MDP (all p < 0.05). No associations were observed between physical activity and BMC and BMD in children with high adherence to the MDP. In conclusion, engaging in moderate to vigorous physical activity and reducing the time spent in sedentary behavior might be particularly beneficial for improving bone health in overweight or obese children with poor adherence to the Mediterranean dietary pattern.