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As complex adaptive systems (CAS), educational systems can be difficult to study authentically with only traditional quantitative or qualitative analytical approaches. The purpose of this paper is to introduce the explanatory sequential longitudinal multi-case conversion (ESLMC) mixed methods research design to provide an example of a methodological innovation for approaching complexity-informed educational research. This design allows researchers to capture interactions of individual components at three levels of four CASs over four years of data collection. In addition, this design allows researchers to capture interactions that occur within and across CAS levels such that researchers can measure, analyze, and interpret new emergent constructs of intertwined influence and their effects on a dependent variable.