The manufacturing method influences the properties of the produced components. This work investigates the influence of manufacturing methods, such as fused deposition modeling (3D printing) and injection molding, on the water absorption and mechanical and thermal properties of the specimens produced from neat bio-based poly(lactic acid) (PLA) polymer and poly(lactic acid)/wood composites. Acrylonitrile butadiene styrene (ABS) acts as the reference material due to its low water absorption and good functional properties. The printing layer thickness is one of the factors that affects the properties of a 3D-printed specimen. The investigation includes two different layer thicknesses (0.2 mm and 0.3 mm) while maintaining uniform overall thickness of the specimens across two manufacturing methods. 3D-printed specimens absorb significantly higher amounts of water than the injection-molded specimens, and the increase in the layer thickness of the 3D-printed specimens contributes to further increased water absorption. However, the swelling due to water absorption in 3D-printed specimens decreases upon increased layer thickness. The tensile, flexural, and impact properties of all of the specimens decrease after water absorption, while the properties improve upon decreasing the layer thickness. Higher porosity upon increasing the layer thickness is the predominant factor. The results from dynamic mechanical analysis and microscopy validate the outcomes. The results from this experimental study highlight the limitations of additive manufacturing.