Abstract Background Clinical Microbiology is a core subject in medical undergraduate curricula. However, students struggle to cover the content and clinically contextualise basic microbiology. Our aim was to evaluate student engagement with new e-learning material and to investigate the impact it had on examination performance in a Clinical Microbiology module. Methods An online resource was designed to support didactic teaching in a Fundamentals of Clinical Microbiology module. One cohort of students had access to the online material (2017/2018 class) and the other did not (2016/2017 class). Each cohort sat the same multiple-choice question (MCQ) and short-note question (SNQ) examination papers and the impact of engagement with the online resource and examination performance was analysed. Results Both groups were of the same academic standard prior to beginning the module. In the 2017/2018 cohort, 227/309 (73.5%) students had ≥80% engagement with the content. Students engaged most with the index of pathogens and pathogen focused clinical cases related to diverse genera and families of clinically important microorganisms. A statistically higher difference in the mean percentage grade in both the MCQ and SNQ examinations was seen for 2017/2018 compared to 2016/2017 cohort. For the MCQ examination, the 2017/2018 cohort were on average 5.57% (95% confidence interval (CI): 3.92 to 7.24%; P < 0.001) higher, and for the SNQ examination the 2017/2018 cohort were on average 2.08% (95% CI: 0.74 to 3.41%; P = 0.02) higher. When the results were adjusted for previous examination performance, for every percentage increase in online engagement the grade in the SNQ examination only increased by 0.05% (95% CI: 0.02 to 0.08) on average. Conclusions These findings suggest students engage with e-learning when studying and that such activities may help students perform better in assessments.