Auto-phosphorylation controls the transition between discrete functional and conformational states in protein kinases, yet the structural and molecular determinants underlaying this fundamental process remain unclear. Here we show that c-terminal Tyr 530 is a de facto c-Src auto-phosphorylation site with slow time-resolution kinetics and strong intermolecular component. On the contrary, activation-loop Tyr 419 undergoes fast kinetics and a cis-to-trans phosphorylation-switch that controls c-terminal Tyr 530 auto-phosphorylation, enzyme specificity and strikingly, c-Src non-catalytic function as a substrate. In line with this, we visualize by X-ray crystallography a snapshot of Tyr 530 intermolecular phosphorylation in which a c-terminal palindromic phospho-motif flanking Tyr 530 on the susbtrate molecule engages the P-loop of the active kinase for ready entry prior catalysis. Perturbation of the phospho-motif accounts for c-Src disfunction as indicated by viral and a colorectal cancer (CRC) associated c-terminal deleted variants. We show that c-terminal residues 531 to 536 are required for c-Src Tyr 530 and global auto-phosphorylation, and this detrimental effect is caused by the susbtrate molecule inhibiting allosterically the active kinase. Our work reveals a bi-directional crosstalk between the activation and c-terminal segments that controls the allosteric interplay between susbtrate and enzyme acting kinases during auto-phosphorylation.