Collagen is a key structural protein in the human body, which undergoes mineralization during the formation of hard tissues. Earlier studies have described the mechanical behavior of bone at different scales, highlighting material features across hierarchical structures. Here we present a study that aims to understand the mechanical properties of mineralized collagen fibrils upon tensile/compressive transient loads, investigating how the kinetic energy propagates and it is dissipated at the molecular scale, thus filling a gap of knowledge in this area. These specific features are the mechanisms that nature has developed to passively dissipate stress and prevent structural failures. In addition to the mechanical properties of the mineralized fibrils, we observe distinct nanomechanical behaviors for the two regions (i.e., overlap and gap) of the D-period to highlight the effect of the mineralization. We notice decreasing trends for both wave speeds and Young's moduli over input velocity with a marked strengthening effect in the gap region due to the accumulation of the hydroxyapatite. In contrast, the dissipative behavior is not affected by either loading conditions or the mineral percentage, showing a stronger damping effect upon faster inputs compatible to the bone behavior at the macroscale. Our results offer insights into the dissipative behavior of mineralized collagen composites to design and characterize bioinspired composites for replacement devices (e.g., prostheses for sound transmission or conduction) or optimized structures able to bear transient loads, for example, impact, fatigue, in structural applications.