This study aimed at co-encapsulating borage seed oil (BSO)- and peppermint oil (PO) blends in ultrasound-assisted complex nanoparticles stabilized by soy protein isolate (SPI) and purity gum ultra (PGU) in different ratios: SPI/PGU-1:0 (NP1), 0:1 (NP2), 1:1 (NP3), 1:3 (NP4), and 3:1 (NP5). The BSO- and PO-loaded SPI/PGU complex nanoparticles (BP-loaded SPNPs) coded as NP4 (SPI-PGU-1:3) revealed a zeta potential of -33.27 mV, a PDI of 0.14, and the highest encapsulation efficiency (81.38 %). The main interactions observed among SPI, PGU, BSO, PO, and a blend of BSO and PO, as determined by FTIR and molecular docking, involved hydrophobic effects, electrostatic attraction, and H-bonding. These interactions played crucial roles in the production of BP-loaded SPNPs. XRD results validated the alterations in the structure of BP-loaded SPNPs caused by varying proportions of SPI and PGU. The thermal capacity of BP-loaded SPNPs (NP4), as determined by TGA, exhibited the lowest amount of weight loss compared to other BP-loaded SPNPs. Morphological results revealed that NP4 and NP5 exhibited a spherical surface and two distinguishable layers, indicating successful coating of PGU onto the droplet surface. In addition, BP-loaded SPNPs (NP4) exhibited a higher antioxidant effect due to their improved progressive release and prolonged release of co-encapsulated BSO and PO during in vitro digestion. The comprehensive investigation of the co-encapsulation of BSO and PO in complex nanoparticles, dietary supplements, and double-layered emulsified systems provides valuable insights into the development of functional foods.