Identifying the structural rearrangement and the active sites in photo-induced reactions is a fundamental challenge to understand from a microscopic perspective the underlying dynamics ruling the functional mechanisms of heme proteins. Here, femtosecond stimulated Raman spectroscopy is used to follow the ultrafast evolution of two 1 six-coordinate heme proteins. By exploiting the sensitivity of Raman spectra to the structural conguration, we investigate the eects of photolysis and binding of amino acid residues in cytochrome c and neuroglobin. Comparing the system response for different time delays and Raman pump resonances, we show how details of atomic motions and energy redistribution can be unveiled.