BACKGROUND: Clinical supervision makes an important contribution to high quality patient care and professional wellbeing for the allied health workforce. However, there is limited research examining the longitudinal implementation of clinical supervision for allied health. The aim of this study was to determine the effectiveness of clinical supervision for allied health at a regional health service and clinicians' perceptions of the implementation of an organisational clinical supervision framework. METHODS: A cross-sectional study was conducted as a phase of an overarching participatory action research study. The Manchester Clinical Supervision Scale (MCSS-26) tool was used to measure clinical supervision effectiveness with additional open-ended questions included to explore the implementation of the clinical supervision framework. MCSS-26 findings were compared with an initial administration of the MCSS-26 5 years earlier. MCSS-26 data (total scores, summed domain and sub-scale scores) were analysed descriptively and reported as mean and standard deviation values. Differences between groups were analysed with independent-samples t-test (t) and one-way between groups ANOVA. RESULTS: There were 125 responses to the survey (response rate 50%). The total MCSS-26 score was 78.5 (S.D. 14.5). The total MCSS-26 score was unchanged compared with the initial administration. There was a statistically significant difference in clinical supervision effectiveness between speech pathology and physiotherapy (F = 2.9, p = 0.03) and higher MCSS-26 scores for participants whose clinical supervisor was a senior clinician and those who chose their clinical supervisor. Seventy percent of participants perceived that the organisation's clinical supervision framework was useful and provided structure and consistent expectations for clinical supervision. CONCLUSIONS: Clinical supervision was effective for allied health in this regional setting and clinical supervision effectiveness was maintained over a 5 year period. The implementation of an organisational clinical supervision framework may have a positive effect on clinical supervision for some professions.