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The present study investigates the impacts a sudden change to online instruction had on undergraduates’ motivation and learning and reveals challenges to students’ engagement in emergency remote learning. Through reflexive thematic analysis, we identified three overarching reasons for students’ difficulties with engagement: Feeling Disconnected, Distracted, and Discordant; Struggling to Engage amidst Lost Autonomy and Personal Stressors; and Experiencing Academic Burden and Burnout. We discuss the implications of these findings as they pertain to abrupt environmental changes, online learning, and students’ self-regulation. Our conclusions highlight the importance that learning contexts and social connectedness have on undergraduates’ willingness and ability to enact self-regulated learning behaviors and strategies.