Described are methods of removing phospholipids and other off-flavor-causing compounds from edible proteins using a cyclodextrin treatment. The methods include treating soy protein with cyclodextrins such as β-cyclodextrin to form cyclodextrin-compound complexes and then separating the resulting complexes from the protein. Optionally, prior to treating the protein with cyclodextrin, the protein is sonicated and then treated with a phospholipase, such as phospholipase A2. Versions of the methods described herein are capable of removing more than 99% of phospholipids from soy protein.