One challenging need for inspection capabilities is in adhesively bonded joints between composite components, a common location of premature failure in aerospace structures. In this work we demonstrate that dynamic, full-spectral scanning of FBG sensors embedded in the adhesive bond can identify changes in bond quality through the measurement of non-linear dynamics of the joint. Eighteen lap joint specimens were fabricated with varying manufacturing quality. Ten samples also included fiber Bragg grating (FBG) sensors embedded in the adhesive bond for real-time inspection during a simulated flight condition of these single-lap joints. Prior to testing, pulse phase thermography imaging of the pristine specimens revealed defects such as air bubbles, adhesive thickness variations, and weak bonding surface between the laminate and adhesive. The lap joint specimens were then subjected to fatigue loading, with regular interrogation of the FBG sensors at selected load cycle intervals. The FBG data was collected during vibration loading of the lap joint to represent an in-flight environment. Changes in the lap joint dynamic response, including the transition to non-linear responses, were measured from both the full-spectral and peak wavelength FBG data. These changes were correlated to initial manufacturing defects and the progression of fatigue-induced damage independently measured with pulse phase imaging and visual inspections of the failure surfaces.