Background <p>The high-value utilization of soy protein isolate (SPI), hemp seed protein (HPP) and pea protein isolate (PPI) in conjugate food systems are limited due to their inherent functional defects.</p> Methods <p>A systematic comparison was conducted between the effects of ultrasound-assisted Maillard reaction and traditional wet-heat treatment on the multiscale structure and functional properties of covalent conjugates formed between isomaltooligosaccharide (IMO) and SPI (SPI-IMO), HPP (HPP-IMO) or PPI (PPI-IMO).</p> Results <p>According to the circular dichroism (CD) spectroscopy results, the α-helix or β-turn content of SPI, HPP and PPI decreased upon glycosylation, while the content of β-sheet or random coil showed an increasing trend. Compared with the traditional wet-heat treatment, the grafting degrees of the SPI-IMO, HPP-IMO and PPI-IMO prepared assisting with ultrasound treatment increased from 15.29 ± 0.63%, 15.53 ± 0.64% and 15.62 ± 0.51% to 30.12 ± 0.44%, 30.09 ± 0.61% and 31.82 ± 0.30%, respectively, while their solubilities increased from 61.96 ± 0.55%, 25.98 ± 1.68% and 53.65 ± 1.03% to 89.9 ± 1.05%, 45.46 ± 1.72%, 84.85 ± 0.99%. And SPI-IMO conjugates showed excellent foaming properties and emulsifying properties. Although PPI-IMO conjugates exhibited a higher degree of grafting (DG) value than SPI-IMO conjugates, SPI-IMO conjugates demonstrated superior foaming and emulsifying properties, confirming that the intrinsic properties of proteins play a decisive role in functional improvement.</p> Conclusions <p>This research showed that ultrasound-assisted Maillard reaction takes unique advantages in modifying HPP and opened up a new path for its high-value utilization.</p> Graphical abstract <p></p>