With ultrasonic fatigue testing (UFT), it is possible to investigate the damage initiation and accumulation from the weakest link of the composite material in the very high cycle fatigue (VHCF) regime in a shorter time frame than conventional fatigue testing. However, the thermal influence on the mechanical fatigue of composites and the scatter in fatigue data for composites under ultrasonic cyclic three-point bending loading still need to be investigated. In this study, we conducted interrupted constant-amplitude fatigue experiments on a carbon-fiber satin-fabric reinforced in poly-ether-ketone-ketone (CF-PEKK) composite material. These experiments were carried out using a UFT system, which operates at a cyclic frequency of 20 kHz with a pulse–pause sequence. Various parameters, such as the CF-PEKK specimen’s surface temperature, acoustic activity, and the ultrasonic generator’s input resonance parameters, were measured during cyclic loading. During experiment interruption, stiffness measurement and volumetric damage characterization in the CF-PEKK specimens using 3D X-ray microscopy (XRM) were performed. The locations of damage initiation and accumulation and their influence on the changes in in situ parameters were characterized. Under fixed loading conditions, damage accumulation occurred at different locations, leading to scattering in fatigue life data. Further, the damage population decreased from the surface to the bulk of the composite material.