The research work aims to compare the physical and mechanical properties of biodegradable polybutylene adipate terephthalate (PBAT), polycaprolactone (PCL), and poly(lactic acid) (PLA) fabricated via fused deposition modeling (FDM) and conventional compression molding (CM) method. It was found that the thermal stability was comparable for sample fabricated using both techniques. The percentage difference for the density measurement was 7.4%. The water absorption of FDM samples was about 75.5% higher compared to those fabricated using the CM due to higher porous structures obtained. The results also showed that the FDM did not significantly affect the materials' crystallinity, however the flowability increases by 25.2%. The tensile strength, tensile modulus, elongation at break (E b ), impact strength, and water contact angle of FDM samples were approximately 25.5%, 25.0%, 46.4%, 50.3%, and 20.7% lower compared to the CM samples.