Additive manufacturing (AM) is used to fabricate polymeric materials into complex three-dimensional (3D) structures. As the 3D structure is built by sequential layer-by-layer deposition of filaments dispensed from a translating nozzle (in the case of extrusion-based printing), defects often form at the filament-filament interface. The out-of-equilibrium structural development that occurs during the printing process is difficult to directly measure by quantitative means, limiting our understanding of the physical mechanisms at play. Here, we utilize in operando X-ray photon correlation spectroscopy (XPCS) measurements with microbeam capability to probe the real-time structural evolution at the filament-filament interface during extrusion 3D printing. We investigate the solidification of a dual-cure (UV/thermal) acrylate/epoxy resin during multilayer 3D printing as a rational model by tracking the nanoscale motion of filler particles embedded in the resin. The spatially and temporally resolved dynamics (on length scales from several nm to a few hundreds of nm and time scales of 10–3 < t < 103 seconds) are measured during the deposition of a single filament as well as during the deposition of a second layer on top of the cured underlayer. The addition of a second layer introduces structural perturbations at the interface and results in accelerated interfacial dynamics compared to those of the cured underlayer. However, as time proceeds, the local dynamical heterogeneity disappears, and the evolution of the dynamics progresses uniformly within the entire interfacial region. The homogeneity across the interface results from the formation of an interpenetrated epoxy network that spans across the first and second filaments. This homogeneous interface is responsible for the isotropic tensile properties of a 3D-printed sample that are independent of print direction and nearly the same as the bulk (non-3D-printed) sample. The XPCS microrheology approach provides insight into the dynamics-process-property relationship at the printed filament interfaces.