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Critical thinking and higher-order thinking skills (HOTS) are essential competencies for higher education graduates to remain competitive in the 21st century. However, numerous studies in Indonesia indicate that students often struggle to demonstrate these skills effectively, partly due to lecturers’ pedagogical practices. This study investigates the extent to which lecturers in Indonesian higher education institutions balance the use of lower-order thinking skills (LOTS) and higher-order thinking skills (HOTS) in their teaching and assessment practices. Employing a case study design, data were collected from three disciplinary fields—English, Religion, and History. A total of 120 documents were analyzed, including 60 course outlines and 60 past examination papers, supplemented by two rounds of classroom observations for each discipline over one semester. Data were analyzed using frequency counts, percentages, and log-likelihood analysis, with results visualized through pie and bar charts. The findings reveal that while lecturers exhibit an overall epistemic orientation toward fostering HOTS—such as creativity, criticality, collaboration, and communication—these orientations are not consistently reflected in classroom discourse or assessment practices. Notably, History lecturers demonstrated a greater reliance on LOTS-oriented instruction compared to their counterparts in English and Religion. The study underscores the need for pragmatic and innovative approaches to instructional and assessment design that more effectively cultivate HOTS. It recommends that Indonesian higher education institutions provide sustained professional development for lecturers and invest in digital technologies and adequate infrastructure to support transformative and higher-order learning.