Mechanical energy in the form of ultrasound, and protein complexes intuitively have been considered as two distinct unrelated topics. However, in the past few years, increasingly more attention has been paid to the ability of ultrasound to induce chemical modifications on protein molecules that further change protein‐protein interaction and protein self‐assembling behavior. Despite efforts to decipher the exact structure and the behavior‐modifying effects of ultrasound on proteins, our current understanding of these aspects remains limited. The limitation arises from the complexity of both phenomena. Ultrasound produces multiple chemical, mechanical, and thermal effects in aqueous media. Proteins are dynamic molecules with diverse complexation mechanisms. This review provides an exhaustive analysis of the progress made in better understanding the role of ultrasound in protein complexation. It describes in detail how ultrasound affects an aqueous environment and the impact of each effect separately and when combined with the protein structure and fold, the protein‐protein interaction, and finally the protein self‐assembly. It specifically focuses on modifying role of ultrasound in amyloid self‐assembly, where the latter is associated with multiple neurodegenerative disorders.