Research has documented the use of tools in computer-based learning environments as problematic, that is, learners do not use the tools and when they do, they tend to do it suboptimally. This study attempts to disentangle cause and effect of this suboptimal tool use for experienced learners. More specifically, learner variables (metacognitive and motivational) were related to the tool presentation (non-/embedded), interventions, type of tool use (quantitatively and qualitative) and learners’ performance. One hundred and seventeen graduate students were assigned to one of five conditions (embedded and non-embedded with explained tool functionality, embedded and non-embedded with non-explained tool functionality and one control condition) to study a hypertext using semi-structured concept maps as the tools. Findings are discussed with respect to experienced learners’ role on tool use and performance. Although no differences among conditions and performance were found, results reveal that the self-regulation skill of organization and the explained tool functionality affected time on tool negatively, while the self-regulation skill of elaboration and perceived tool usability showed a positive effect. Time on tool influenced performance positively. Quality influenced performance negatively. It is argued that some tools and interventions are unnecessary for experienced learners.