In this study, olive pit agro-waste from the olive oil industry is valorized by incorporating it as an additive in a polyethylene terephthalate glycol (PETG) matrix to develop bio-based composite materials for large format additive manufacturing (LFAM). The olive pits were first ground into olive pit powder (OPP) and then functionalized by polymerizing poly(butylene adipate-co-terephthalate) PBAT on their surface, resulting in a hydrophobic, modified olive pit powder (MOPP) with enhanced compatibility with the PETG matrix. OPP and MOPP composites were compounded and 3D-printed via Fused Granular Fabrication (FGF) using 5, 10, and 15 wt.% concentrations. The PBAT coating increased the degradation temperature and specific heat capacity of the material, contributing to a lower melt viscosity during printing, as confirmed by MFR, MDSC, and TGA analyses. Tensile testing revealed that MOPP composites generally exhibited superior mechanical properties compared to OPP composites, likely due to the improved compatibility between PBAT on the MOPP surface and the PETG matrix. SEM analysis further validated these findings, showing a highly irregular and porous fracture surface in OPP composites, while MOPP composites displayed a smooth surface with well-integrated MOPP in the PETG matrix.