BackgroundClinical practice guidelines risk having little impact on healthcare if not effectively implemented. Theory informed, targeted implementation may maximise their impact. Our study explored barriers to and facilitators of guideline implementation and use by South African primary care nurses and allied healthcare workers in four provinces in South Africa. We also proposed interventions to address the issues identified.MethodsWe used qualitative research methods, comprising focus group discussions using semi-structured topic guides. Seven focus group discussions were conducted (48 providers) in four South African provinces (Eastern Cape, Western Cape, Kwazulu-Natal, Limpopo). Participants included mostly nurses, dieticians, dentists, and allied health practitioners, from primary care facilities in rural and peri-urban settings. The analysis proceeded in three phases. Firstly, two analysts conducted inductive thematic content analysis to develop themes of data. This was followed by fitting emergent themes to the Theoretical Domains Framework and finally to the associated Behaviour Change Wheel to identify relevant interventions.ResultsParticipants are knowledgeable about guidelines, generally trust their credibility and are receptive and motivated to use them. Guidelines are seen by nurses to provide confidence and reassurance, as well as professional authority and independence where doctors are scarce. Barriers to guideline use include: inadequate systems for printed book distribution, insufficient and substandard photocopies, linguistic inappropriateness (e.g. complicated language, lack of summaries, unavailable in local languages), unsupportive auditing procedures, limited involvement of end-users in guideline development, and patchy training that may not filter back to all providers. Future aspirations identified include: improving the design features of guidelines, accessible places to find guidelines, making digitally-formatted versions available, more supplementary materials (e.g. posters) to support patient engagement, accessible clinical support following training, and in-facility training for all professional cadres to ensure fair access, similar levels of capability and interdisciplinary consistency.ConclusionsSouth African primary care nurses and allied health practitioners have high levels of motivation to use guidelines, but face many systemic barriers. We used the Behaviour Change Wheel to suggest relevant, implementable interventions addressing identified barriers. This theory-informed approach may improve clinical guideline implementation and impact healthcare for South Africa.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3778-2) contains supplementary material, which is available to authorized users.