Commencing students in universities today are very diverse with regards to their academic preparation, language, and cultural background. Some of these students are also first in family to attend university. With such diverse student profiles and previous learning experiences, it is possible that some students may not be confident to employ the academic literacies required in their study program. This paper reports on a mixed-method case study undertaken at an Australian university, to explore commencing students' confidence in using academic literacies at the start of their study program and after they had completed two semesters of instruction. Data were collected from 120 students at Time 1 and 54 students at Time 2 of the study. The study found that some students were uncertain of completing some task types such as case studies, article reviews and critical reflections. Students also lacked confidence employing discipline-specific vocabulary, critical thinking, and critical writing skills. Although, students' confidence levels in employing academic literacies improved overall after two semesters of instruction, confidence in writing critically appeared to remain low. Furthermore, students with English as an additional language (EAL), those studying externally and students who had taken a break from their studies, identified challenges in multiple areas of academic literacies.