It has been suggested that Content and Language Integrated Learning (CLIL) positively affects learners’ content-related vocabulary. While CLIL has become increasingly popular throughout Spain, the language of instruction in this learning environment has predominantly been English, largely to the neglect of other languages. Calls have consequently been made to conduct comparative research across other languages to better understand the strengths and weaknesses of CLIL irrespective of the language of instruction. In addition, female learners have been found to outperform males in areas of vocabulary such as lexical availability (LA) in English. However, given suggestions that CLIL may blur gender differences, it is unclear whether this difference is also found in a multilingual CLIL context. This study thus aims to determine whether an English advantage is observed in LA in a multilingual CLIL environment, and whether this advantage varies in male and female learners. Results indicate that there is a clear dominance in English over French, regardless of gender. However, analysis across different grades reveals that CLIL instruction has a clear effect on the students’ LA in different languages, but in different ways for male and female learners. The findings are of key importance to CLIL stakeholders wishing to support male and female learners in multilingual classrooms.