Iron (Fe) is the most abundant transition metal ion in the human body and its role, in the form of heme, has been implicated in Alzheimer's disease (AD) and type 2 diabetes mellitus (T2Dm). Heme binds both amyloid beta (Aβ) and human islet amyloid polypeptide (hIAPP) to form heme-Aβ and heme-hIAPP complexes, respectively, and form reactive oxygen species (ROS) like H2O2, O2-etc., which are known to cause oxidative damage. However the intermediates involved during ROS formation have not yet been isolated. In this study the oxygen bound intermediates of both heme-Aβ(1-16) and heme-hIAPP(1-19) have been isolated and characterized using absorption, EPR and resonance Raman (rR) spectroscopy. Fe-O stretches have been found at 575 cm-1 and 577 cm-1 for heme-Aβ(1-16) and heme-hIAPP(1-19) respectively. The oxy intermediates are stable at low temperatures. The isolation of the intermediates reveals a mechanistic pathway of ROS generation through the two heme complexes.