The integration of inquiry-based learning and pedagogical deep learning in teaching modules is important for supporting meaningful and student-centered science learning in elementary schools. However, evidence remains limited regarding how consistently these approaches are represented together in teaching modules developed by pre-service elementary teachers. This study examined the quality of inquiry-based teaching modules integrating pedagogical deep learning developed by pre-service elementary teachers at Yogyakarta State University, Indonesia. A qualitative document analysis approach was employed to examine 15 teaching modules selected purposively from a population of 39 modules developed in a science education course. The analysis was guided by six stages of inquiry-based learning and three dimensions of pedagogical deep learning: meaningful, mindful, and joyful learning. The findings showed that five modules (33.3%) were classified as high quality, seven (46.7%) as medium quality, and three (20%) as needing improvement. Orientation, data collection, and conclusion-drawing activities were generally well represented, whereas problem formulation and hypothesis formulation were less consistently incorporated. Meaningful learning was the most frequently represented dimension, while mindful learning was absent from 10 of the 15 modules. These findings provide evidence of variation in how inquiry-based learning and pedagogical deep learning are incorporated into teaching modules. The study contributes an integrated analytical perspective for identifying strengths and areas for improvement in pre-service teachers’ module design. The findings may inform teacher education activities aimed at strengthening the design of inquiry-based and pedagogically deep learning-oriented materials. However, because the study examined written modules from a purposively selected sample, it does not directly establish pre-service teachers’ readiness to implement STEM learning in classrooms.