We investigated whether the implementation of a scaffolded case study assignment could increase student perceptions of their scientific literacy (SL) skills in a third year Nutritional Science course. The change in students' SL perceptions were assessed by the completion of two surveys (administered at the start and end of the semester) consisting of questions probing a range of SL criteria relevant to undergraduate students. Additionally, we determined if the change in student perceived SL over the semester i) was related to their learning approach (i.e. deep versus surface approaches), as assessed by the Revised Two-Factor Study Process Questionnaire-2 (R-SPQ-2F), and ii) differed between course format, that is, in-class traditional lecture (LEC) and online distance education (DE). The LEC students (n = 179) showed improvements in all ten SL outcomes assessed over the course of the semester, whereas the DE students (n = 71) showed improvements in only six of the ten parameters assessed, however, the DE course started with a higher assessment of baseline SL capabilities. Additionally, the overall change in perceived SL capabilities was not associated with learning approach (i.e. surface or deep) in either class format. These data demonstrate that case-based learning assignments can promote students perceived SL capabilities in both traditional lecture and distance education course formats.