Multiple heat treatments of polycaprolactone (PCL) during processing cycles can exert a significant influence on both the mechanical and biological properties of filaments intended for 3D printing via Fused Deposition Modeling (FDM). This phenomenon is particularly critical for materials designed for biomedical applications, such as tissue engineering scaffolds, where unintended degradation can lead to a loss of biocompatibility and structural integrity. The primary objective of this research was to systematically evaluate the effects of repeated extrusion on PCL variants with three distinct molecular weights: 25 kDa, 37 kDa, and 50 kDa. To simulate realistic manufacturing and recycling conditions, the materials underwent a multi-stage extrusion process consisting of three successive cycles. The characterization included measurements of filament diameter consistency, thermal stability via Differential Scanning Calorimetry (DSC), mechanical properties through tensile testing, and comprehensive cell viability assays (XTT) using the Saos-2 cell line, with all results verified by one-way ANOVA and Tukey’s post-hoc tests. The results demonstrated that the impact of repeated heat treatment depends strictly on the molecular weight. PCL 50 kDa exhibited a gradual decline in mechanical and biological properties, suggesting limitations for its extensive reuse in high-precision medical contexts without additional stabilization. Conversely, the PCL 37 kDa variant showed remarkable stability across all cycles, maintaining its structural and functional integrity (p>0.05). Furthermore, PCL 25 kDa showed improved cytocompatibility (p<0.001), supporting the "thermal cleaning" hypothesis. Overall, PCL 37 kDa emerged as the most reliable grade for sustainable, multi-cycle additive manufacturing in tissue engineering.