Analogies between non-trivial topologies of matter and light have inspired numerous studies, including defect formation in structured light and topological photonic band-structures. Three-dimensional topological objects of localized particle-like nature attract broad interest across discipline boundaries from elementary particle physics and cosmology to condensed matter physics. Here we show how simple structured light beams can be transformed into optical excitations of atoms with considerably more complex topologies representing three-dimensional particle-like Skyrmions. This construction can also be described in terms of linked Hopf maps, analogous to knotted solitons of the Skyrme-Faddeev model. We identify the transverse polarization density current as the effective magnetic gauge potential for the Chern-Simons helicity term. While we prepare simpler two-dimensional baby-Skyrmions and singular defects using the traditional Stokes vectors on the Poincaré sphere for light, particle-like topologies can only be achieved in the full optical hypersphere description that no longer discards the variation of the total electromagnetic phase of vibration.