The current study examines the role of cognitive and perceptual individual differences (i.e., aptitude) in second language (L2) pronunciation learning, when L2 learners’ varied experience background is controlled for. A total of 48 Chinese learners of English in the UK were assessed for their sensitivity to segmental and suprasegmental aspects of speech on explicit and implicit modes via behavioural (language/music aptitude tests) and neurophysiological (electroencephalography) measures. Subsequently, the participants’ aptitude profiles were compared to the segmental and suprasegmental dimensions of their L2 pronunciation proficiency analyzed through rater judgements and acoustic measurements. According to the results, the participants’ segmental attainment was associated not only with explicit aptitude (phonemic coding), but also with implicit aptitude (enhanced neural encoding of spectral peaks). Whereas the participants’ suprasegmental attainment was linked to explicit aptitude (rhythmic imagery) to some degree, it was primarily influenced by the quality and quantity of their most recent L2 learning experience.