Methodology is at the heart of effective English for Academic Purposes (EAP) instruction, yet it has attracted limited empirical research. This study, therefore, pursued two main goals: to design a questionnaire to analyze the cognitive skills of classroom activities and to investigate the skills that EAP practitioners focus on in their teaching. To this end, a 40-item questionnaire was developed based on Bloom’s Revised Taxonomy (2001) on a five-point Likert scale and was validated with SmartPLS. It was distributed to 78 EAP instructors, both EFL and content teachers, in Iran. Four EAP classes were also observed twice so that teachers' real practices could be explored based on the model. The final exams developed by the same teachers were also analyzed. The results showed that the majority of EAP teachers believed that often in EAP classes they focus on teaching and testing activities that develop all levels of cognitive skills. The EFL teachers claimed to focus on higher-level cognitive skills in teaching more frequently than the content teachers did. Yet, the results of class observations and test analysis revealed that the lower cognitive levels, including remembering and understanding, were the target of the EAP courses. The findings can mostly be explained by teachers' perceptions, pedagogical knowledge, and familiarity with course design and learners' needs. They promise implications for EAP course design, methodology, and teacher training.