3,3’-Diindolylmethane (DIM) is a bioactive compound found in Cruciferous vegetables that possesses health benefits such as antioxidant, anticancer, and anti-inflammatory effects. However, hydrophobicity and photolabile limit its pharmaceutical applications. This study aims to prepare and characterize DIM-encapsulated whey protein isolate (WPI) nanoparticles mixed at different ratios of WPI and DIM using the combined heating–ultrasound method. Results showed that all the samples showed adequate physicochemical characteristics: The mean particle size of the nanoparticles could be controlled down to 96–157 nm depending on the DIM to WPI ratio used in the preparation with a low polydispersity index (<0.5), higher negative values of zeta potential (>−40 mV) as well as with greater encapsulation efficiency (>82%). Flow behavior indices showed the shear-thinning Non-Newtonian or pseudoplastic (n < 1) behavior of the nanoparticles. The thermal properties were characterized by differential scanning calorimetry (DSC), which showed that DIM was successfully entrapped in WPI nanoparticles. The secondary structure of WPI was changed after DIM incorporation; electrostatic interaction and hydrogen bonding were major facilitating forces for nanoparticles formation, confirmed by Fourier Transform Infrared Spectroscopy (FT-IR). Transmission electron microscopy (TEM) micrographs showed that all the samples had a smooth surface and spherical structure. The wall material (WPI) and encapsulation method provide effective protection to DIM against UV light and a broad range of physiologically relevant pH’s (2.5, 3.5, 4.5, 5.5, and 7). In conclusion, whey protein isolate (WPI)-based nanoparticles are a promising approach to encapsulate DIM and overcome its physicochemical limitations with improved stability.