Interspecific hybrid crude palm oil (HCPO) HIE OxG derived from crossbred African oil palm (Elaeis guineensis) and American Caiaué (Elaeis oleifera) is prominent for its fatty acid and antioxidant compositions (carotenoids, tocopherols, and tocotrienols), lower production cost, and high pest resistance properties compared to crude palm oil. Biodegradable and sustainable encapsulants derived from vegetable byproducts were used to formulate HCPO nanoparticles. Nanoparticles with hybrid crude palm oil and jackfruit seed flour as a wall material (N-JSF) and with hybrid crude palm oil and jackfruit axis flour as a wall material (N-JAF) were optimized using a 22 experimental design. They exhibited nanoscale diameters (<250 nm) and were characterized based on their zeta potential, apparent viscosity, pH, color, and total carotenoid content. The nanoparticles demonstrated a monodisperse distribution, good uniformity, and stability (polydispersity index < 0.25; zeta potentials: N-JSF −19.50 ± 1.47 mV and N-JAF −12.50 ± 0.17 mV), as well as high encapsulation efficiency (%) (N-JSF 86.44 ± 0.01 and N-JAF 90.43 ± 1.34) and an optimal carotenoid retention (>85%). These nanoparticles show potential for use as sustainable and clean-label HCPO alternatives in the food industry.