Three-dimensional woven fabric-reinforced composites (3DWFRCs) offer promising potential for advanced lightweight structural applications due to their superior impact resilience, structural integrity, and enhanced damage tolerance. This study investigates the influence of weave architecture such as, binder yarn pathway, number of stuffer layers, fiber-volume-fraction of multi-directional reinforcement in preforms, and inter-yarn crossover points on the low-velocity impact (LVI) behavior of E-glass roving/epoxy-based 3DWFRCs. A comparative analysis was performed across different weave configurations of 3D woven preforms, all fabricated at constant areal density. Following the controlled LVI events, specimens were subjected to post-impact characterization, including compression-after-impact (CAI) testing. Results reveal that woven architectures with fewer inter-yarn crossovers, longer binder yarn floats, and a reduced yet proportionally consistent stuffer-to-binder ratio demonstrated superior transverse impact resistance, owing to improved energy dissipation and minimized resin-rich zones. An increase in stuffer layers in preform generally augments energy absorption capacity; however, a saturation threshold was observed beyond which further additions yield marginal gains, primarily constrained by porosity-induced degradation in structural efficiency. Architectural parameters, i.e., binder yarn pathway and stuffer layers, have been shown to critically dictate the low-velocity impact behavior of 3DWFRCs, revealing key structure–property correlations.