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. We present the first mouse bone phosphoproteome of 8- and 73-week-old mice following acute in vivo insulin stimulation and identified >16,000 phosphorylation sites of which >4,600 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 evolutionary conservation analysis and integration with human GWAS enabled us to prioritise novel kinase substrates highly likely to play important roles in bone function. We next developed a semi-high throughput CRISPR/Cas9 loss-of-function screen in zebrafish to interrogate these novel phosphorylation events and the regulation of bone formation. We present ongoing results from this functional screen and we hope our functional analysis of the phosphoproteome will further enhance our understanding of the signalling mechanisms controlling bone biology and whole-body energy metabolism.