This dataset is linked to the NSW Koala Research Plan–funded project 2022_01: Vaccination of Koalas at the Interface between Chlamydia positive and Chlamydia negative koala populations. It comprises plasma IgG responses, cytokine concentrations, clinical disease scores, and Chlamydia pecorum shedding measurements collected during a 24 month field vaccination trial. Data were analysed using Linear Mixed Effects Models and Cumulative Link Mixed Models. The dataset underpins the following publication: Simpson, S.J., Higgins, D.P., Timms, P. et al. (2025). Evaluation of Chlamydia pecorum major outer membrane protein vaccine as a management tool in wild koala (Phascolarctos cinereus) populations. Scientific Reports, 15, 30601. https://doi.org/10.1038/s41598-025-13296-6