Instructional videos risk overloading learners' limited working memory resources due to the transient information effect. Learner control is one way to mitigate this concern, but has shown almost zero overall effect and considerable heterogeneity. Consequently, it is essential to identify when learner control is most beneficial. The present study examined the influence of cues on learners' behaviour, cognitive process, metacognition and learning performance in an interactive learning environment. Employing a 2 (temporal cues: without vs. with) × 2 (organizational cues: without vs. with) between-subject design, 117 participants were randomly assigned to one of four conditions: no cues, temporal cues, organizational cues and temporal cues + organizational cues. Among these, temporal cues (ie, progress bar) serve as time-related signals designed to regulate pacing, and organizational cues (ie, table of contents) provide a structural framework for the content. Significant cueing effects were observed for both cue types at germane cognitive load and transfer. Notably, our results indicate that organizational cues effectively guide learners' attention towards the underlying structure, thus promoting cognitive processing. These unique benefits are evident in improved topic recall, retention and monitoring accuracy. Importantly, combined temporal cues and organizational cues were seen to not only allow learners to exhibit more engagement behaviours (ie, skimming) but also assist learners in accurately judging their learning. These findings strongly support the recommendation to use cues to enhance the effectiveness of learner control.