Childhood obesity is an increasingly prevalent global health concern associated with significant metabolic, endocrine, and skeletal consequences. During critical periods of growth and peak bone mineralisation, excessive adiposity may impair skeletal development by disrupting bone formation and remodeling. The effects of obesity on bone metabolism are complex and multifactorial, involving altered mechanical loading, hormonal dysregulation, and chronic low-grade inflammation. Key mediators, including insulin resistance, adipose tissue dysfunction, and disturbances in calcium–phosphate–magnesium–vitamin D homeostasis, contribute to impaired osteoblastic and osteoclastic activity. Additionally, gut microbiome dysbiosis and reduced nutrient absorption may exacerbate skeletal fragility and abnormal mineralisation. This review provides an integrative overview of current evidence regarding the impact of obesity on the developing skeleton. It discusses (I) methods of bone assessment in children with excess body weight and associated diagnostic challenges, (II) biomarkers relevant to bone metabolism and obesity-related skeletal alterations, (III) the role of dietary factors, nutrient intake, and physical activity in bone development, and (IV) future research directions aimed at reducing fracture risk and improving skeletal health outcomes in paediatric populations.