Content and language integrated learning (CLIL) has captured the attention of both teachers and researchers (Dalton-Puffer, 2017; Pavón Vázquez, & Méndez García, 2017; San Isidro, 2018; Otto & Estrada, 2019). However, while research interests have predominantly focused on the comparison between CLIL and EFL students’ competence, there seems to be a need to explore the methodological approaches that best trigger the learning of language and content in CLIL settings. The aim of this exploratory study is to analyze how CLIL lessons using different methodological approaches influence students’ perception of learning as well as learning outcomes. Participants were a total of fifty primary-school students from year six (25 in a CLIL classroom where the teacher followed a teacher-directed teaching approach and 25 students in another classroom where the teacher followed a task-based approach). A total of 20 CLIL sessions of Science were observed, and while data on students’ learning outcomes were collected by means of a writing task, perceptions on learning were collected by means of students learning diaries and semi-structured interviews. Findings from the study show that students’ perception of learning is higher in those CLIL sessions where the teacher follows the traditional approach of presentation, practice and production. However, learning outcomes, measured in students’ written production, show that students under the task-based approach outperformed those students following a traditional methodology in content, vocabulary, and textual organization, but not in grammar, spelling and mechanism. In addition, our results show that traditional methodology triggers explicit learning, since students report learning specific language items, while TBLT triggers content learning and implicit language learning. Finally, our findings suggest that teacher training courses should draw attention to the impact of different methodological approaches, and encourage the use of teaching strategies that draw attention to both language and content.