The composition variation in composites' structure can be customized to expand their applications for antennae, capacitors, and heat transfer devices. In this study, a fused deposition modeling technique was utilized to customize composition variation in a polylactic acid–copper composite structure. The significant differences in constituents' thermal properties can induce defects and residual stresses, limiting composites' fracture toughness. This property can be improved by post-manufacturing processes such as microwave-assisted heat treatment of composites containing constituents with different dielectric properties. In this work, samples involving a composite part sandwiched between two symmetrical polymer sections were additively manufactured. The composite layers were deposited after selective impregnation of a polylactic acid filament surface with micro-size copper particles. Four sets of manufactured samples were exposed to a 2.45 GHz microwave with 3 kW power for 30, 60, 75, and 90 s. The tensile fracture test results showed that 75 s of exposure improved the interlayer fracture toughness of composites significantly by 37%, the highest among all treatment conditions. Based on microscopy and thermal analysis, it was discussed that decreasing the size of microvoids in the layers, the percentage of polymer crystallinity, and residual stress would benefit fracture toughness of exposed composites.