The pedagogical approach--Content and Language Integrated Learning (CLIL)--has been widely adopted around the globe with its dual aims of developing students' second language (L2) proficiency and mastering content knowledge simultaneously. However, its effectiveness remains inconsistent. This inconsistency has led researchers to call for an investigation into the perspectives of CLIL students to understand the factors behind the success and failure of CLIL implementation. To address this gap, this study explores CLIL students' perspectives through the lens of self-regulation and examines the relationships between CLIL students' self-regulation levels, linguistic challenges, and learning outcomes. Involving 167 junior secondary students from three schools in Hong Kong that adopted different CLIL models in Hong Kong, the study revealed moderate self-regulation levels and varying linguistic challenges among CLIL students, with listening being identified as the most difficult skill. A significant, moderately positive correlation was found between self-regulation levels and perceived linguistic challenges. Multiple regression analysis also found that motivation was a key predictor of both L2 proficiency and content subject achievement, while other self-regulation constructs (self-preparation, self-monitoring, and self-reflection) showed non-significant predictive values. Pedagogical implications are provided to develop students' self-regulation skills and address perceived linguistic challenges, ultimately enhancing the learning experience and outcomes for CLIL students of diverse abilities.