Background People under the age of 65 in clinical risk groups are at increased risk of severe complications and death from influenza. In England, influenza vaccine coverage rates in this cohort remain profoundly low. This qualitative study aimed to explore (1) the reasons that underly suboptimal influenza vaccine uptake among different clinical risk groups in England and (2) how healthcare providers and commissioners perceive the feasibility and acceptability of integrating the influenza vaccine programme in non-primary care settings. Methods The study consisted of two phases. Phase I involved 32 semi-structured interviews conducted with individuals from three clinical risk groups: diabetes, chronic liver disease or chronic respiratory disease (or comorbidities). Phase II consisted of semi-structured interviews with 50 healthcare providers based in National Health Service primary and secondary care settings, and influenza vaccine commissioners and programme managers. Data were analysed thematically. Results Access was not the primary issue underlying suboptimal vaccine uptake among participants in clinical risk groups, who instead cited low-risk perceptions of influenza infection and deficits of information about the relevance of vaccination for their condition management. Healthcare providers in non-primary care settings rarely discussed or recommended influenza vaccination across patient pathways, despite being able to address the concerns raised by participants in clinical risk groups. Healthcare providers were positive about the potential to offer vaccine recommendations and delivery, but questions remain around feasibility. Conclusion Patient pathways are punctuated with varying opportunities to discuss or deliver influenza vaccines during the winter season, though the commissioning and organisation of chronic disease management shapes how clinical risk groups interface with primary/secondary tiers of healthcare services. Embedding vaccine delivery in non-primary care settings may help to reduce inequalities and offer patients at risk the information and consent pathways they desire but is not a cost-neutral innovation and requires resource allocation.