<p>Additive manufacturing (AM) is increasingly being explored not only for prototyping and model fabrication, but also for producing end-use components. Among various AM techniques, material extrusion is widely adopted due to its accessibility and versatility; however, a limitation of this approach is anisotropic mechanical properties - in particular reduced strength in the interlayer direction. This study explores the application of atmospheric cold plasma treatment to enhance the wettability and mechanical performance of Fused Filament Fabrication (FFF) 3D printed parts. By integrating a plasma treatment wand within a 3D printer, the effects of in-situ plasma treatment are explored on two polymers: polylactic acid (PLA), and thermoplastic polyurethane (TPU). Plasma-treated samples exhibit significantly improved surface wettability, with water contact angles decreasing by more than 50%, indicating enhanced hydrophilicity. Significant improvement in strength in the interlayer direction was observed for PLA samples and in particular for PLA-TPU where the material also changed between layers and is attributed to the formation of reactive functional groups on the polymer surfaces. Wedge shear testing using cylindrical samples further supports these findings, showing that plasma-treated multi-material PLA/TPU coupons demonstrate a 63% increase in the maximum force required for shearing. By enhancing the surface energy and interlayer welding, plasma treatment helps to address the relative weaknesses in interlayer strength, making it valuable for applications requiring higher performance 3D printed components.</p>