© 2022 Elsevier B.V.This study presents a facile strategy for architecting the interface morphology to create tougher and stronger interfaces in additively manufactured multi-material polymer composites. A sutural interfacial morphology between two dissimilar polymer phases PLA (hard) and TPU (soft) is designed and fabricated by the fused filament fabrication technique. The proposed strategy utilizes one of the process parameters (i.e., overlap distance) to create sutural interfaces with soft protrusions. The microscopic inspections of the interface suggest that the proposed strategy can control the protrusion amplitude, which indirectly influences the interfacial defect density. A positive correlation between the overlap distance and resulting protrusion amplitude is obtained. The interfacial toughness measurements by the double cantilever beam test reveal a linear correlation between the interfacial toughness and protrusion amplitude. The proposed interfacial architecture can result in up to a 16–18-fold increase in the interfacial toughness in comparison with the baseline interface. Three distinct toughening mechanisms associated with the fracture of the proposed interfaces are identified: (1) geometric toughening associated with the interface roughness, (2) enhancement of the intrinsic interfacial toughness due to the reduced interfacial defect density between the PLA and TPU, and (3) additional plastic (or inelastic) energy dissipation within the TPU layer. The results reported in this study are anticipated to provide guidelines to produce multi-material polymer composites with stronger and tougher interfaces via additive manufacturing.