Analyzing the integration of scientific knowledge to guide decision-making processes supporting design challenges in engineering education is critical. However, effectively engaging in informed design decision-making processes is challenging, particularly in the context of online education. Simulation-based learning can bring authentic design practices to online education, but effective guidance and scaffolding must be provided to learners. Therefore, this research investigates the implications of integrating simulation-based learning with an argumentation framework to guide students in incorporating scientific knowledge into their design decisions, particularly in designing energy-efficient housing. This study took place during online learning due to the COVID-19 pandemic and was implemented within a first-year engineering technology undergraduate course. It aimed to analyze students’ decision-making processes when designing a zero-energy home for a Midwestern city using Aladdin, an integrated CAD/CAE platform that can be used to design a structure and simulate its function within a single system. This study investigates how students informed their decision-making processes in design for energy-efficient homes and the recurring trends in students’ designs related to economic decision making and energy science. The overall results show how cost constraints significantly influenced students’ observation and argumentation processes during their design challenge, highlighting the pivotal role of economic considerations in shaping their decision making. Moreover, the findings underscore the importance of holistic approaches in providing insights into teaching strategies for online learning, particularly in navigating the intersection of scientific and economic factors in design challenges.