Biological structures integrate morphometry (shape-based rules) with materials design to maximize organism survival. The exoskeleton of the armored fish, Polypterus senegalus, balances flexibility with protection from predatory and territorial threats. Material properties of the exoskeleton are known; however, the geometric design rules underlying its anisotropic flexibility are uncharacterized. Here, we show how scale shape, articulation, and composite architecture produce anisotropic mechanics using bio-inspired, multi-material 3D-printed prototypes. Passive loading (draping) shows that compliant connections between the scales contribute to mechanical anisotropy. Simulated and experimental active loading (bending) show orientation-dependent stiffness ranging over orders of magnitude, including ‘mechanical invisibility’ of the scales where they do not add stiffness to the exoskeleton. The results illustrate how morphometry provides a powerful tool to tune flexibility in composite architectures independent of varying constituent materials composition. We anticipate that introducing morphometric design strategies will enable flexible, protective systems tuned to complex shapes and functions.