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Abstract Background The Ethiopian Primary Healthcare Clinical Guidelines (EPHCG) seek to improve quality of primary health care, while also expanding access to care for people with Non-Communicable Diseases and Mental Health Conditions (NCDs/MHCs). The aim of this study was to identify barriers and enablers to implementation of the EPHCG with a particular focus on NCDs/MHCs. Methods A mixed-methods convergent-parallel design was employed after EPHCG implementation in 18 health facilities in southern Ethiopia. Semi-structured interviews were conducted with 10 primary healthcare clinicians and one healthcare administrator. Organisational Readiness for Implementing Change (ORIC) questionnaire was self-completed by 124 health workers and analysed using Kruskal Wallis ranked test to investigate median score differences. Qualitative data were mapped to the Consolidated Framework for Implementation Science (CFIR) and the Theoretical Domains Framework (TDF). Expert Recommendations for Implementing Change (ERIC) were employed to select implementation strategies to address barriers. Results Four domains were identified: EPHCG training and implementation, awareness and meeting patient needs (demand side), resource constraints/barriers (supply side) and care pathway bottlenecks. The innovative facility-based training to implement EPHCG had a mixed response, especially in busy facilities where teams reported struggling to find protected time to meet. Key barriers to implementation of EPHCG were non-availability of resources (CFIR inner setting), such as laboratory reagents and medications that undermined efforts to follow guideline-based care, the way care was structured and lack of familiarity with providing care for people with NCDs-MHCs. Substantial barriers arose because of socio-economic problems that were interlinked with health but not addressable within the health system (CFIR outer setting). Other factors influencing effective implementation of EPHCG (TDF) included low population awareness about NCDs/MHCs and unaffordable diagnostic and treatment services (TDF). Implementation strategies were identified. ORIC findings indicated high scores of organisational readiness to implement the desired change with likely social desirability bias. Conclusion Although perceived as necessary, practical implementation of EPHCG was constrained by challenges across domains of internal/external determinants. This was especially marked in relation to expansion of care responsibilities to include NCDs/MHCs. Attention to social determinants of health outcomes, community engagement and awareness-raising are needed to maximize population impact.