In this study, the effect of dual modification using ultrasound (100 and 300 W for 5, 10, and 15 min) and microwave (600 W for 45 s) treatments on functional properties of wheat gluten protein (WGP) and whey protein concentrate (WPC), as two by-products of food industry with different primary functional properties, was investigated. Ultrasound treatment did not affect the solubility of both proteins significantly but the emulsion and foam properties were increased up to 10 min. Nevertheless, microwave treatment after ultrasound caused a significant decrease in the solubility of both proteins. However, the foam stability of the WPC and WGP was not significantly modified after microwave treatment. The obtained results showed a more positive effect of ultrasound at 100 W for 10 min than other ultrasound treatments on the functional and structural properties of both proteins. The zeta potential of both proteins was decreased after dual physical modifications, but thermal stability of proteins was improved after microwave treatment.