Many universities have implemented initiatives to drive instructional change, yet their success has often been limited due to a lack of recognition of academia as a complex dynamic system. This paper explores how the interconnected and dynamic nature of academic systems influences faculty motivation to adopt instructional innovations, such as project-based learning (PBL) and small group collaborations (SGCs). We present a Conceptual Systems Dynamics Model (CSDM) that illustrates these interconnections, demonstrating how systemic factors create feedback loops that either reinforce or hinder faculty motivation, as well as other related factors. These loops, represented as Causal Loop Diagrams (CLDs), were derived from literature reviews and qualitative data obtained from interviews and focus groups involving 17 faculty and administrators within an Engineering Department at a research university in South America. The paper identifies thirteen CLDs, comprising seven reinforcing dynamics that positively influence faculty motivation and six balancing dynamics that exert negative pressure. Using empirical evidence and analysis, we describe how the systemic factors influence faculty motivation, and how shifts in motivation reciprocally impact these interconnected factors. By elucidating the complex dynamics at play, this research contributes to a deeper understanding of how to promote sustainable instructional change within academic institutions.