Abstract Objective To identify whether the clinical maturity of medical trainees impacts upon the level of trainee competency in evidence-based medicine (EBM). Materials and methods Undergraduate and graduate-entry medical trainees entering their first year of training in the clinical environment were recruited for this study. Competency in EBM was measured using a psychometrically validated instrument. EBM competency scores were analysed using Student's t tests, in order to differentiate between undergraduate and graduate-entry trainee performance. Ten focus group discussions were conducted with undergraduate and graduate-entry trainees. Audio transcripts were thematically analysed. Results Data on a total of 885 medical trainees were collected over a 5-year period. Undergraduate trainees had significantly higher EBM competency scores during years in which the programme was presented in a didactic format (mean difference (MD)=1.24 (95% CI)CI 0.21 to 2.26; 1.78 (0.39 to 3.17); 2.13 (1.16 to 3.09)). Graduate trainee EBM competency scores increased when a blended learning approach to EBM was adopted, demonstrating no significant difference in EBM competency scores between undergraduate and graduate cohorts (−0.27 (−1.38 to 0.85); −0.39 (−1.57 to 0.79). Qualitative findings indicated that differences in learning and teaching preference among undergraduate and graduate-entry trainees influenced the level of competency obtained in EBM. Conclusions Clinical maturity is the only one factor that may influence medical trainees' competency in EBM. Other predictors of EBM competency may include previous training and exposure to epidemiology, biostatistics and information literacy. While graduate-entry medical students may have more ‘life’ experience, or maturity, it does not necessarily translate into clinical maturity and integration into the clinical environment.