Representational competence in science is the ability to generate external representations (e.g. equations, graphs) of real-world phenomena, transform between these representations, and use them in an integrated fashion. Difficulties in achieving representational competence are often considered central to difficulties in learning science. Representational competence is indicative of domain expertise and is characterised by distinct problem-solving strategies. Eye-tracking studies have consistently demonstrated that experts employ unique perceptual attention (e.g. gaze-fixation) patterns while solving problems that involve different external representations. Here, we present a different strand of evidence, indicating that perceptual navigation patterns (eye movements) mark representational competence in science, in more specific ways than attention. Gaze behaviours of chemistry professors (experts) and undergraduate students (novices) were tracked as they individually performed a multi-representational-categorisation task and a chemical equation-balancing task. The following three-step analysis was performed on these data: (i) First, we independently calibrated the levels of representational competence of our participants through their performance in the categorisation task. (ii) Then, we compared these competence levels with the participants’ perceptual patterns (gaze behaviour) exhibited during the categorisation task. (iii) Finally, we analysed whether the identified perceptual patterns were specific to representational competence, or more general, through the results of the equation-balancing task. Our analysis of perceptual navigation (eye movements) provided further support to previous findings showing gaze-behaviour differences between experts and novices. Going further, our analysis indicated that experts deploy distinct eye-movement patterns, but specifically during representational competence-related problems. This suggests that representational competence is an embodied skill that fundamentally changes the tuning of the perceptual system, as argued by recent ‘field’ theories of cognition.