The graduate chemical engineering curriculum at our institution Elmergib University is replete with both problem-based and project-based learning components. This paper focuses on a complex methodology of inquiry-based learning (IBL), which has been proven to well prepare graduate students for a successful career in engineering. IBL requires Students to invest a considerable time during the class and after working at home learning with the aid of mentoring how to develop and answer a research question. Teaching both IBL and the development of field-specific simulation skills challenge professors. That does not allow much of the class time required to cover material reliance on mathematical tools that often hamper student understanding of the underlying phenomena and difficulty in providing immersive and exciting visuals that support in-depth learning. An IBL component was incorporated into a simulation-based design in four successive graduate courses: Advanced computational Numerical Methods, Advanced heat transfer, Advanced fluid mechanics, and Advanced transport phenomena. The courses were modified to contain Multiphysics simulations with application building that develop technical competency by developing modeling skills, deeper understanding by solving realistic problems, and writing skills by producing technical reports for each simulation. The use of the Multiphysics application building component adds a new skillset that further strengthens our program graduates. The paper shows the teaching and learning strategies efforts have been implemented, course teaching tools Apps structure, student outcome assessment, and research project exam questions and their simulation results from students’ reports.