It is not yet clear on whether the fracture characteristics of structured composite capsules and homogeneous nanoagglomerates differ significantly under impact loading conditions. Experimental measurement of impact fracture properties of such small agglomerates is difficult, due to the length and time scales associated with this problem. Using computer simulations, here we show that nanoagglomerates are subjected to normal impact loading fracture within a few nanoseconds in a brittle manner. The restitution coefficient of the nanoagglomerates varies nonlinearly with initial kinetic energy. The fracture of nanoagglomerates does not always happen at the moment when they experience the maximum wall force, but occurs after a time lag of a few nanoseconds as characterised by impact survival time (IST) and IST index. IST is dependant on the initial kinetic energy, mechanical and geometric properties of the nanoagglomerates. For identical geometries of the capsules, IST index is higher for capsules with a soft shell than for these with a hard shell, an indication of the enhanced ability of the soft nanocapsules to dissipate impact energy. The DEM simulations reported here based on theories of contact mechanics provide fundamental insights on the fracture behaviour of agglomerates—at nanoscale, the structure of the agglomerates significantly influences their breakage behaviour.