Polyamide 6,6 (PA66)-based biocomposites with low-cost carbonaceous natural fibers (i.e., soy hulls, co-product from soybean industry) were prepared through twin-screw extrusion and injection molding. The soy hull natural fiber was pyrolyzed at two different temperatures (500 °C and 900 °C denoted as BioC500 and BioC900 respectively) to obtain different types of biocarbons. The BioC500 preserved a higher number of functional groups as compared to BioC900. Higher graphitic carbon content was observed on the BioC900 than BioC500 as evident in Raman spectroscopy. Both biocarbons interact with the PA66 backbone through hydrogen bonding in different ways. BioC900 has a greater interaction with N-H stretching, while BioC500 interacts strongly with the amide I (C=O stretching) linkage. The BioC500 interrupts the crystallite growth of PA66 due to strong bond connection while the BioC900 promotes heterogeneous crystallization. Dynamic mechanical analysis shows that both biocarbons result in an increasing storage modulus and glass transition temperature with increasing content in the BioC/PA66 biocomposites over PA66. Rheological analysis shows that the incorporation of BioC900 results in decreasing melt viscosity of PA66, while the incorporation of BioC500 results in increasing the melt viscosity of PA66 due to greater filler–matrix adhesion. This study shows that pyrolyzed soy hull natural fiber can be processed effectively with a high temperature (>270 °C) engineering plastic for biocomposites fabrication with no degradation issues.