This study offers a systematic process structure property comparison of polylactic acid (PLA) nanocomposites reinforced with hybrid carbon nanotubes (CNT) and graphene oxide (GO), fabricated via pellet-fed fused granular fabrication (FGF) and conventional filament-based material extrusion (MEX). Nanocomposites were prepared via a dissolution assisted route to ensure homogeneous filler dispersion while mitigating thermal degradation. To bridge formulation and extrudability, the melt flow index (MFI) was introduced as a critical processability metric alongside standardized thermal (TGA/DSC) and mechanical (tensile/flexural) characterization. Hybrid reinforcement, through complementary CNT and GO mechanisms, significantly enhanced thermal stability, elevating the onset degradation temperature from 305.0 °C to 319.8 °C, and promoted crystallization, increasing the degree of crystallinity from ∼7.5% to 21.5%. Tensile strength improved by 8–22% and elongation at break by up to 82% , despite a moderate reduction in elastic modulus (7–29%) . Flexural modulus increased by up to 41% (MEX) and 28% (FGF), while FGF specimens exhibited markedly higher bending compliance and deformation capability, correlating with slightly higher interlayer porosity from FESEM. MFI decreased with nanofiller addition, with the MWCNT-rich formulation showing the largest viscosity increase, while FGF feedstocks exhibited higher MFI than MEX filaments due to reduced thermomechanical history. FGF achieved thermal, rheological, and mechanical performance comparable to MEX, with microstructural differences providing a beneficial stiffness-ductility trade-off. This work provides the first comparative dataset incorporating MFI for identical hybrid formulations across both processing routes, establishing pellet-fed FGF as a scalable, cost-effective, and environmentally friendlier alternative to filament-based MEX for high-performance additive manufacturing.