An integrated approach through coupling response surface method (RSM) and genetic algorithm (GA) was applied to optimize the spray dryer operational condition for production of fish oil microcapsules. The inlet drying air temperature, aspirator rate, and peristaltic pump rate were independent and encapsulation efficiency (EE) and exergy efficiency were dependent variables. RSM was applied to establish the relationship between the independent and dependent variables followed by integrating the developed models using three mathematical approaches and measure the fitness value of GA. Consequently, the optimal drying condition for microencapsulation of fish oil was: inlet drying air temperature = 177.23°C, aspirator rate = 63.93%, and peristaltic pump rate = 14.04% yielding exergy efficiency of 8.10% and EE of 79.14%. The results of confirmation experiments for selected drying condition proved the capability of utilized approach for determination of sustainable and qualified process in fish oil microencapsulation by spray drying.