Reading primary literature is a popular classroom practice that exposes students to the process of science. However, the analysis of primary literature can be taxing and time-consuming for students. For this reason, it is important to determine the source of student challenges and what motivates them to read primary literature. To better understand students’ challenges, preferences, and motivations towards analyzing primary literature, we held focus groups with biology undergraduates where we asked them about their thoughts and perceptions on this practice. Students felt they struggle with understanding the big picture of an article, certain aspects of scientific literacy like data interpretation and experimental setup, and lack of knowledge of terms and techniques. Further analysis of the data using the achievement goal and expectancy-value theories of motivation revealed that students: 1) demonstrate mastery and performance approach goal orientations, which are typically associated with positive learning outcomes, 2) value the usefulness of reading primary literature, and 3) feel most engaged in the process of reading an article when the topic interests them. We provide pedagogical recommendations based on our findings.