We investigate the influence of quenched disorder on the dynamic structure factor of Heisenberg bilayers on the square, triangular, and kagome lattice in the quantum paramagnetic phase. Perturbative continuous unitary transformations and white graphs are employed to calculate the one-triplon contribution up to high orders in perturbation about the dimer limit for bimodal and continuous disorder. For the square lattice we find that the lifetime of the gap mode is increased by stronger quantum correlations while stronger disorder effects are observed for the triangular lattice due to geometric frustration. For intra-dimer disorder, in-band energy gaps are observed for both lattices which can be understood in terms of a level repulsion on dimers with low and high intra-dimer exchange that are close in energy at the momentum where the in-band gap opens. For the highly frustrated kagome lattice disorder even allows to decrease the gap energy. In addition, the localization length of the low-energy flat band is increased up to order 7 in perturbation theory. The interplay of quenched disorder, geometric frustration, and strong correlations leads therefore to rich structures in the dynamical structure factor of two-dimensional quantum magnets.