The development of eco-friendly, mechanically stable, and biocompatible materials for medical packaging has gained significant attention in recent years. Halloysite nanotubes (HNTs) have emerged as a promising nanomaterial due to their unique tubular structure, high aspect ratio, and biocompatibility. We aim to develop a novel soybean oil-based thermoset bio-resin incorporating HNTs and to characterize its physical and functional properties for medical packaging. Soybean oil was epoxidized using an eco-friendly method and used as a precursor for preparing the thermoset resin (ESOR). Different amounts of HNTs (0.25, 0.50, and 1.0 wt.%) were used to prepare the ESOR/HNTs blends. Various characteristics such as transparency, tensile strength, thermal resistance, and water absorption were investigated. While incorporating HNTs improved the tensile strength and thermal properties of the ESOR, it noticeably reduced its transparency at the 1.0 wt.% level. Therefore, HNTs were modified using sodium hydroxide and (3-Aminopropyl) triethoxysilane (APTES) and ESOR/HNTs blends were made using 1.0 wt.% of modified HNTs. It was shown that modifying HNTs using NaOH improved the transparency and mechanical properties of prepared blends compared to those with the same amount of unmodified HNTs. However, modifying using (3-Aminopropyl) triethoxysilane (APTES) decreased the transparency but improved the water absorption of prepared resins. This study provides valuable insights into the design of HNT-based ESOR blends as a sustainable material for medical packaging, contributing to the advancement of eco-friendly packaging solutions in the healthcare industry.