Aggregation of egg and wheat proteins during cake mixing and baking was monitored by SE-HPLC after sequential extraction of dough and baked cakes in SDS-buffer first and then in SDS/DTE buffer. Three cake recipes were compared, including either only egg, only flour, or both flour and egg proteins. Dough mixing did not result in any changes in protein solubility or size distribution. Baking promoted protein aggregation and quickly resulted in the solubility loss of all proteins within the first extracting solvent with the exception of wheat omega gliadins. Upon baking similar kinetics of proteins solubility loss in SDS-buffer were observed regardless of cake recipes. Extraction of the remaining SDS-insoluble proteins with SDS/DTE buffer allowed total protein recovery but only in the case of cakes made on the basis of only flour. For cakes including eggs and despite the presence of DTE a disulfide reducing agent, very large polymers were release into solution, contrarily to the only flour cakes where only small polypeptides (>70,000 g/mol) were mostly recovered. Protein sequential extraction combined with SE-HPLC analysis highlighted the critical role of egg proteins in triggering wheat and egg proteins complexation into SDS-insoluble aggregates stabilized through disulfide but also non-reducible covalent bonds. •Cake protein aggregation during processing was studied using SE-HPLC.•Dough mixing does not impact the size distribution of egg and flour proteins.•Egg and flour proteins formed mixed aggregates upon baking.•Mixed aggregates are stabilized by thiol/disulfide and iso-peptide bonds.•Eggs proteins contribute to strengthen the cake protein network.