<p>Additive manufacturing, particularly fused filament fabrication (FFF), has become an important technique for producing lightweight and geometrically complex polymer structures, yet the reliable integration of these parts into structural assemblies requires effective joining strategies. Adhesive bonding offers significant advantages over mechanical fastening by enabling uniform stress transfer and compatibility with dissimilar materials, but the mechanical integrity of bonded 3D-printed joints is strongly influenced by both adherend material and joint geometry. This study explores the effects of adherend material (PLA and PETG) and joint geometry, single lap joint (SLJ), notched SLJ (NSLJ), and curved joint (CJ) on failure loads and fracture behavior. Specimens were manufactured via fused filament fabrication (FFF) and bonded using a methacrylate-based structural adhesive. A cohesive zone model (CZM) was developed to simulate load–displacement responses and predict failure initiation and progression. The novelty of this work lies in the combined experimental and numerical investigation of how joint geometry and material selection affect the mechanical integrity of bonded 3D-printed components. Among the tested configurations, curved joints showed the highest failure loads, while notched joints performed the weakest. CZM simulations accurately predicted experimental behavior, with deviations ranging from 1.03% to 9.77%. Failure modes varied with both material and geometry, including adhesive cohesive failure and adherend fracture. These findings offer a framework for enhancing the reliability of polymer bonded joints in additive manufacturing, supporting failure prevention through informed design.</p>