Although the architectural design parameters of 3D-printed polymer-based scaffolds—porosity, height-to-diameter (H/D) ratio and pore size—are significant determinants of their mechanical integrity, their impact has not been explicitly discussed when reporting bulk mechanical properties. Controlled architectures were designed by systematically varying porosity (30–75%, H/D ratio (0.5–2.0) and pore size (0.25–1.0 mm) and fabricated using fused filament fabrication technique. The influence of the three parameters on compressive mechanical properties—apparent elastic modulus Eapp, bulk yield stress σy and yield strain εy—were investigated through a multiple linear regression analysis. H/D ratio and porosity exhibited strong influence on the mechanical behavior, resulting in variations in mean Eapp of 60% and 95%, respectively. σy was comparatively less sensitive to H/D ratio over the range investigated in this study, with 15% variation in mean values. In contrast, porosity resulted in almost 100% variation in mean σy values. Pore size was not a significant factor for mechanical behavior, although it is a critical factor in the biological behavior of the scaffolds. Quantifying the influence of porosity, H/D ratio and pore size on bench-top tested bulk mechanical properties can help optimize the development of bone scaffolds from a biomechanical perspective.