Long-range electronic order descending from a metallic parent state constitutes a rich playground to study the intricate interplay of structural and electronic degrees of freedom. With dispersive and correlation features as multifold as topological Dirac-like itinerant states, van-Hove singularities, correlated flat bands, and magnetic transitions at low temperature, kagome metals are located in the most interesting regime where both phonon and electronically mediated couplings are significant. Several of these systems undergo a charge density wave (CDW) transition, and the van-Hove singularities, which are intrinsic to the kagome tiling, have been conjectured to play a key role in mediating such an instability. However, to date, the origin and the main driving force behind this charge order is elusive. Here, we use the topological bilayer kagome metal ScV6Sn6 as a platform to investigate this puzzling problem, since it features both kagome-derived nested Fermi surface and van-Hove singularities near the Fermi level, and a CDW phase that affects the susceptibility, the neutron scattering, and the specific heat, similarly to the siblings AV3Sb5 (A = K, Rb, Cs) and FeGe. We report on our findings from high-resolution angle-resolved photoemission, density functional theory, and time-resolved optical spectroscopy to unveil the dynamics of its CDW phase. We identify the structural degrees of freedom to play a fundamental role in the stabilization of charge order. Along with a comprehensive analysis of the subdominant impact from electronic correlations, we find ScV6Sn6 to feature an instance of charge density wave order that predominantly originates from phonons. As we shed light on the emergent phonon profile in the low-temperature ordered regime, our findings pave the way for a deeper understanding of ordering phenomena in all CDW kagome metals.