The aim of this work was to evaluate the influence of high-intensity ultrasound (HIUS) treatment on whey protein isolate (WPI) molecular structure as a previous step for complex coacervation (CC) with kappa-carrageenan (KC) and its influence on CC functional properties. Protein suspension of WPI (1% w/w) was treated with an ultrasound probe (24 kHz, 2 and 4 min, at 50 and 100% amplitude), non HIUS pretreated WPI was used as a control. Coacervation was achieved by mixing WPI and KC dispersions (10 min). Time and amplitude of the sonication treatment had a direct effect on the molecular structure of the protein, FTIR-ATR analysis detected changes on pretreated WPI secondary structure (1600–1700 cm−1) after sonication. CC electrostatic interactions were detected between WPI positive regions, KC sulfate group (1200–1260 cm−1), and the anhydrous oxygen of the 3,6 anhydro-D-galactose (940–1066 cm−1) with a partial negative charge. After ultrasound treatment, a progressive decrease in WPI particle size (nm) was detected. Rheology results showed pseudoplastic behavior for both, KC and CC, with a significant change on the viscosity level. Further, volume increment, stability, and expansion percentages of CC foams were improved using WPI sonicated. Besides, HIUS treatment had a positive effect on the emulsifying properties of the CC, increasing the time emulsion stability percentage. HIUS proved to be an efficient tool to improve functional properties in WPI-KC CC.