Undergraduate STEM lecture courses enroll hundreds who must master declarative, conceptual, and applied learning objectives. To support them, instructors have turned to active learning designs that require students to engage in "self-regulated learning" (SRL). Undergraduates struggle with SRL, and universities provide courses, workshops, and digital training to scaffold SRL skill development and enactment. We examined two theory-aligned designs of digital skill trainings that scaffold SRL and how students' demonstration of metacognitive knowledge of learning skills predicted exam performance in biology courses where training took place. In Study 1, students' (n = 49) responses to training activities were scored for quality and summed by training topic and level of understanding. Behavioral and environmental regulation knowledge predicted midterm and final exam grades; knowledge of SRL processes did not. Declarative and conceptual levels of skill-mastery predicted exam performance; application-level knowledge did not. When modeled by topic at each level of understanding, declarative knowledge of behavioral and environmental regulation and conceptual knowledge of cognitive strategies predicted final exam performance. In Study 2 (n = 62), knowledge demonstrated during a redesigned video-based multimedia version of behavioral and environmental regulation again predicted biology exam performance. Across studies, performance on training activities designed in alignment with skill-training models predicted course performances and predictions were sustained in a redesign prioritizing learning efficiency. Training learners' SRL skills--and specifically cognitive strategies and environmental regulation--benefited their later biology course performances across studies, which demonstrate the value of providing brief, digital activities to develop learning skills. Ongoing refinement to materials designed to develop metacognitive processing and learners' ability to apply skills in new contexts can increase benefits.