We present analytic approaches for examining students’ learning processes related to sun–Earth–moon phenomena. 6th-grade students conducted investigations in Inq-ITS, an NGSS-aligned simulation environment that generates real-time assessments of inquiry competencies from students’ interaction data Fine-grained logfile data were used to examine whether the order of activities influenced inquiry processes in subsequent investigations. Analyses revealed progressions in hypothesis- and data-collection practices, including control-of-variables strategy, and increasingly sophisticated mental models. These findings demonstrate how simulation-based environments and logfile analyses can provide insights into how students learn complex astronomical phenomena beyond traditional concept inventories.