This study offers a comparative evaluation of the impact of carbon fiber reinforcement on polypropylene (PP) and polylactic acid (PLA) matrices, focusing on their application in fused deposition modeling (FDM). Composite filaments with varying micro carbon fiber (MCF) contents were fabricated for both matrices, with their mechanical, moisture absorption, and morphological properties thoroughly characterized. In PP composites, MCF addition significantly improved tensile and flexural strengths, achieving optimal enhancement at 9.09 wt%, where tensile and flexural strengths rose by 75% and 100%, respectively, compared to pure PP. Conversely, PLA composites showed slight strength increases at lower MCF contents (below 5 wt%) but experienced strength reductions as fiber content exceeded this threshold. However, both materials exhibited increased stiffness (elastic modulus) with rising MCF levels, though PLA achieved optimal strength at a lower fiber loading. Moisture absorption increased in both matrices as fiber content rose; PP showed a proportional increase, whereas PLA displayed more pronounced absorption due to inter- and intra-filament porosities. Optical microscopy (OM) highlighted further differences: PP retained fiber distribution and bonding over a wide range of MCF levels, while PLA showed strong fiber adhesion and ductile fracture behavior at lower MCF, shifting to brittle fracture and void formation at higher levels. Gaussian Process Regression (GPR) modeling corroborated these trends, identifying optimal MCF content as 9.09 wt% for PP and around 2.5 wt% for PLA. These findings provide guidance on selecting material and fiber loading for FDM applications, with each material achieving a unique balance of mechanical performance and moisture resistance.