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The aim of this work was to evaluate the influence of high intensity ultrasound (HIUS) treatment on the molecular conformation of whey protein isolated (WPI) as a previous step for complex coacervation with iota carrageenan (IC) and its effect on the surface functional properties of complex coacervates (CC). Both biopolymers were hydrated (1% w/w) separately. A WPI suspension was treated with an ultrasonic bath (40 kHz, 600 W, 30 and 60 min, 100% amplitude). A non-sonicated protein was used as a control. Coacervation was achieved by mixing WPI and IC dispersions (10 min). FTIR-ATR analysis (400–4000 cm−1) detected changes after sonication on WPI secondary structure (1600–1700 cm−1), electrostatic interaction between WPI and IC by electronegative IC charged groups like sulfate (1200–1260 cm−1), anhydrous oxygen of the 3.6 anhydro-D-galactose (940–1066 cm−1) and the electropositive regions of WPI. Rheology results showed pseudoplastic behavior of both IC and WPI-IC with a significant change in viscosity level. Further, HIUS treatment had a positive effect on the emulsifying properties of the WPI-IC coacervates, increasing the time foaming (30 min) and emulsion stability (1 month) percentage. HIUS and complex coacervation proved to be an efficient tool to improve the surface functional properties of WPI.