Prodigiosin (PG) is a natural compound produced by microorganisms, that is known for its promising bioactive properties. However, owing to its inherent water insolubility, low bioavailability, and poor stability, the practical application of prodigiosin remains challenging. In this work, the nanoparticles of prodigiosin-loaded zein-pectin were prepared using electrostatic deposition and antisolvent precipitation methods. The encapsulation efficiency and loading capacity of prodigiosin in Z-Pet/PG 2:1 nanoparticles were 89.05 % and 7.49 %, respectively, with a zeta potential of -23.03 mV, with a particle size was 184.13 nm. The nanoparticles were uniformly distributed and possessed a spherical morphology, as determined using scanning electron microscopy. The formation mechanism between nanoparticles has been investigated using circular dichroism, fluorescence spectroscopy, molecular docking, and Fourier-transform infrared spectroscopy, which indicated stabilization predominantly through electrostatic, hydrophobic, and hydrogen-bonding interactions. Furthermore, Z-Pet/PG 2:1 nanoparticles proved remarkable stability across a pH range from 3 to 7, NaCl concentrations below 50 mmol/L, at elevated temperatures (60, 70, and 80 °C) for 1 h, and at redispersion. Prodigiosin was progressively delivered by the nanoparticles in simulated gastrointestinal settings, with a cumulative release rate of 75.32 % in simulated intestinal fluid, thereby demonstrating enhanced bioavailability and allowing for a controlled and sustained-release in vitro. These findings indicate that Z-Pet/PG nanoparticles are a promising delivery platform for prodigiosin, and are potentially applicable to other hydrophobic compounds with limited bioavailability.