Numerous adverse effects are reported from excessive usage of synthetic polyolefins including major environmental concerns. Since then, the development of natural-based polymer composites is escalating, to replace the versatile conventional plastics that possess excellent mechanical and thermal properties. Rubber seed shell (RSS) is a novel and abundant natural-based substituent that is highly composed of hemicellulose and cellulose. In this work, we reported on the performance of RSS-filled polypropylene composites added with two different types of compatibilizers: epoxidized vegetable oil (EVO) and phthalic anhydride (PA). The composites were produced using a Haake internal mixer and a compression molding. The tensile, flexural, and impact properties of the composites were analyzed. Later, we investigated the thermal stability and water absorptivity of the composites. The mechanical, thermal, and water absorption properties of the RSS-filled composites deteriorated with increasing RSS loadings. For both EVO and PA-compatibilized systems, the mechanical properties were enhanced except for the elongation-at-break of the composites. PA-compatibilized composites recorded better thermal stability and water absorption resistance under ambient conditions compared to RSS composites with EVO. The qualitative structural evidence of the composites enhanced properties and deterioration were observed using a Zeiss Supra scanning electron microscope. As a novel natural filler, RSS has adequately proven its practicability in manufacturing environmentally friendly natural composites with acceptable mechanical and thermal properties.