The purpose of the present invention is to provide a method for producing a protein composition for suppressing changes such as degradation and denaturation of protein that occur when a highly hydrophilic protein or a protein modified by complete removal of water is subjected to protein irradiation. The method for producing a protein composition of the present invention produces a protein composition containing a protein (A), a radical scavenger (RS), and a compound (HC) capable of forming hydrogen bonds that is one or more selected from the group consisting of amino acids, peptides, and proteins other than the above protein (A), wherein the method for producing a protein composition is characterized in that: the method includes a sterilization step for sterilizing the pre-sterilization protein composition by radiation； the pre-sterilization protein composition contains the protein (A), the radical scavenger (RS), and the compound (HC) capable of forming hydrogen bonds； the protein (A) has one or more functional groups selected from the group consisting of sulfide groups, amide groups, hydroxyl groups, amino groups, and carboxyl groups； the compound (HC) capable of forming hydrogen bonds has one or more functional groups selected from the group consisting of sulfide groups, amide groups, hydroxyl groups, amino groups, and carboxyl groups； the functional groups in the protein (A) and the functional groups in the compound (HC) capable of forming hydrogen bonds can bond by hydrogen bonding； the water content in the pre-sterilization protein composition is 0-30 wt% based on the weight of the pre-sterilization protein composition； the weight ratio of the radical scavenger (RS) and protein (A) in the pre-sterilization protein composition (radical scavenger (RS)/protein (A)) is 0.01-1.0； and the molar ratio of the total number of moles of functional groups of the compound (HC) capable of forming hydrogen bonds and the total number of moles of functional groups of the prote
