Insulin signalling in bone plays a critical role in development and the regulation of energy metabolism. However, a systems biology analysis to map in vivo signalling has yet to be performed. Furthermore, whether signalling is rewired during ageing and insulin-resistance is unknown. Here we present the first mouse bone phosphoproteome study of 8- and 73-week-old mice following acute in vivo insulin stimulation, and identified >16,000 phosphorylation sites, mapped to 4528 bone phosphoproteins, of which >4,600 sites are novel. We observed hundreds of phosphorylation sites differentially regulated between young and old bone revealing dramatic rewiring and defects in insulin signalling. Machine learning coupled to phosphosite evolutionary conservation analysis and integration with human bone mineral density GWAS enabled us to prioritise novel kinase substrates highly likely to play important roles in bone function. We next developed a CRISPR/Cas9 loss-of-function screening pipeline in zebrafish to interrogate these novel phosphorylation events regulating bone development and glucose metabolism. We present ongoing results from this functional screen and hope that our functional analysis of the phosphoproteome will further enhance our understanding of the signalling mechanisms controlling bone biology and whole-body energy metabolism.