Background Screening, brief intervention, and referral to treatment (SBIRT) for risky substance use is infrequently included in routine healthcare in low-resourced settings. A SBIRT programme, adopted by the Western Cape provincial government within an alcohol harm reduction strategy, employed various implementation strategies executed by a diverse team to translate an evidence-based intervention into services at three demonstration sites before broader programme scale-up. This paper evaluates the implementation of this programme delivered by facility-based counsellors in South African emergency centres. Method Guided by the Consolidated Framework for Implementation Research, this mixed methods study evaluated the feasibility, acceptability, appropriateness and adoption of this task-shared SBIRT programme. Quantitative data were extracted from routinely collected health information. Qualitative interviews were conducted with 40 stakeholders in the programme’s second year. Results In the first year, 13 136 patients were screened and 4 847 (37%) patients met criteria for risky substance use. Of these patients, 83% received the intervention, indicating programme feasibility. The programme was adopted into routine services and found to be acceptable and appropriate, particularly by stakeholders familiar with the emergency environment. These stakeholders highlighted the burden of substance-related harm in emergency centres and favourable patient responses to SBIRT. However, some stakeholders expressed scepticism of the behaviour change approach and programme compatibility with emergency centre operations. Furthermore, adoption was both facilitated and hampered by a top-down directive from provincial leadership to implement SBIRT, while rapid implementation limited effective engagement with a diverse stakeholder group. Conclusion This is one of the first studies to address SBIRT implementation in low-resourced settings. The results show that SBIRT implementation and adoption was largely successful, and provide valuable insights that should be considered prior to implementation scale-up. Recommendations include ensuring ongoing monitoring and evaluation, and early stakeholder engagement to improve implementation readiness and programme compatibility in the emergency setting.