Insulin signalling in bone plays a critical role in osteogenesis and in the regulation of whole-body energy metabolism. However, a systems biology analysis to map in vivo signalling network has yet to be performed, and whether this signalling is rewired during ageing and insulin-resistance is still unknown. Here we present the first mouse ageing bone proteome and phosphoproteome of 8- and 73-week-old mice following acute in vivo insulin stimulation and identified >16,000 phosphorylation sites mapped to 4528 bone phosphoproteins, with >4,600 novel phosphosites. Notably, >2100 phosphosites were differentially regulated between young and old bone revealing dramatic rewiring and defects in insulin signalling. Kinase: substrate prediction using machine learning coupled to phosphosite evolutionary conservation analyses and integration with human bone mineral density GWAS enabled us to prioritise novel phosphoproteins conceivable to play important roles in bone biology. We next developed a CRISPR/Cas9 loss-of-function screening pipeline in zebrafish to assess candidate protein function on bone development. This identified several novel insulin-regulated phosphoproteins as causal regulators of bone formation including protein AFF4, the core scaffold of the transcriptional Super Elongation Complex (SEC). Using targeted phosphoproteomics and affinity-purification coupled to mass spectrometry, we show that AFF4 is a novel substrate of P70S6K, and the insulin-regulated phosphosite regulates SEC formation. Furthermore, ChIP-seq revealed the activity of the SEC is defective under insulin-resistant conditions and is associated with reduced phosphorylation of AFF4. Altogether, through in vivo phosphoproteomics and functional genomics we defined in vivo defective insulin-signalling events in old mouse bone and identified novel functional phosphorylation events.