Insulin signalling in bone plays a critical role in development and energy metabolism. Here we present the first mouse bone phosphoproteome study of 8- and 73-week-old mice following acute in vivo insulin stimulation. Hundreds of phosphorylation sites were regulated between young and old bone revealing dramatic rewiring and defects in insulin signalling. We next developed a zebrafish CRISPR/Cas9 loss-of-function screen targeting insulin-regulated phosphoproteins to assess their role in bone mineralisation and development. Several interesting candidates were identified including AFF4, a core scaffold of the Super Elongation Complex (SEC) responsible for driving transcriptional elongation. We show S831 phosphorylation of AFF4 is a novel P70S6K substrate that is dysregulated in aged and insulin-resistant bone, and correlates with reduced transcriptional elongation. Phosphorylation promotes association of ENL/AF9 to the SEC and drives transcription of insulin-dependent target genes required for bone development.