As complex systems approaches to research gain a foothold in educational research, educational researchers may be faced with unique study design challenges. Studies that do not target appropriate levels of analysis or do not capture variable change over time at a fine enough granularity run the risk of missing complex, dynamic, and emergent properties that are the hallmark of complex system behavior. By taking into account context, multiple levels of analysis, and change over time complex systems approaches generate evidence for dynamic processes in education. This paper draws upon three example areas from educational psychology to illustrate important design considerations for conducting complex systems research in education. We discuss how complex systems designs can generate new insight for areas of study such as how psychological constructs influence learning, classroom dynamics, and teacher-student interactions.