Scientific studies have focused on environmentally friendly solutions as effective as the reuse of crop products owing to plastic-waste problems in recent years. This issue is the main driving force for upcoming academic research attempts in waste valorization-related studies. Herein, we integrated an aqua-waste, mussel shell (MS), as a bioadditive form into green thermoplastic polyurethane (TPU) green composites. Tuning of the MS surface was performed to achieve strong adhesion between composite phases. The surface functionalities of MS powders were evaluated via infrared spectroscopy and scanning electron microscopy (SEM) images. Composite samples were prepared by melt-compounding followed by injection molding techniques. It was confirmed by morphological analysis that relatively better adhesion between the phases was achieved for composites involving surface-modified MS compared to unmodified MS. Tensile strength and Young’s modulus of surface-modified MS-filled composites were found to be higher than those of unmodified MS, whereas the elongation at break shifted to lower values with MS inclusions. The shore hardness of TPU was remarkably improved after being incorporated with silane-treated MS (AS-MS). Stearic acid-treated MS (ST-MS) additions resulted in an enhancement in the thermal stability of the composites. Thermo-mechanical analysis showed that the storage moduli of composites were higher than those of unfilled TPU. ST-MS additions led to an increase in the characteristic glass transition temperature of TPU. Melt flow index (MFI) of neat TPU was highly improved after MS loading regardless of modification type. According to the wear test, surface modification of MS displayed a positive effect on the wear resistance of TPU. As the water absorption data of the composites were evaluated, the TPU/AS-MS composite yielded the lowest water absorption. The silane layer on MS inclusion promoted water repellency of composites due to the hydrophobicity of silane. The results of the biodegradation investigation demonstrated that adding unmodified and/or modified MS to the TPU matrix increased the biodegradation rate. The test results at the end of a 7-week period of biodegradation with a soft-rot fungus implied that the composite materials were more biodegradable than pure TPU. Silane modification of MS exhibited better performance in terms of the characterized properties of TPU-based composites.