Alterations in proteins and some functional properties of chicken thigh (TM) and breast meats (BM) cooked with microwave oven (MWO) were evaluated in comparison to traditional electric oven (EO). Cooking loss in both TM and BM did not differ between the cooking methods (p > .05). In TM, MWO cooking resulted in higher water‐holding capacity (WHC) than EO (p < .05). Sarcoplasmic protein solubility of TM decreased with MWO cooking while both cooking methods resulted in reduction in both sarcoplasmic and myofibrillar protein solubility in BM (p < .05). TM and BM cooked with MWO were harder in texture (p < .05) than EO cooked samples as determined in texture profile analysis. The intensity of myofibrillar protein bands in the Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS‐PAGE) decreased after cooking by both MWO and EO, whereas EO cooked samples demonstrated more fragmentation in both sarcoplasmic and myofibrillar proteins in comparison with MWO cooked chicken meats. Practical applications Microwave cooking is an alternative, efficient method to reduce time, energy, and cost as compared to conventional oven cooking. In oven cooking, thermal energy is transmitted quite slow from the surface of the food to the center, whereas microwave energy is converted into heat inside the food itself which provides homogeneous heat distribution. In the present study, the effects of microwave and EO cooking methods on some quality characteristics, mainly proteins of TM and BM were evaluated. It was found that microwave cooking resulted in harder texture, but better WHC to its counterpart which also caused more degradation in myofibrillar and sarcoplasmic proteins. Because microwaves shorten cooking time, lowers the energy consumption, and makes the production process sustainable and more efficient than with conventional ovens, while better preserving the nutritional quality of the product becomes a sound alternative. Therefore, it is worth to keep exploring this novel cooking approach that might render significant advantages in industrial applications.