Background: Influenza vaccination coverage in South Africa is less than 3 % among the general adult population. We explored factors associated with influenza vaccine uptake using the World Health Organization's Strategic Advisory Group on Immunization (SAGE) 3C (confidence, complacency, convenience) model of vaccine hesitancy. Methods: The present study forms part of the Bambisana project, a mixed-methods pre-test-post-test intervention study conducted from 29 April 2023 to 15 April 2024. Participants ≥18 years were enrolled in six Focus Group Discussions (FGDs), stratified by age (≥18–34 and ≥ 35 years). FGDs were audio-recorded, transcribed verbatim, and coded in Dedoose using framework analysis. Results: Among the 48 participants, most (66.7 %, n = 30) were aged 18–34 years, 65.9 % (n = 29) had completed high school, and 70.2 % (n = 33) were unemployed. Overall, influenza vaccine uptake was associated with three key factors: low confidence, high complacency, and a lack of convenience. Low confidence in the influenza vaccine was associated with negative experiences with COVID-19 vaccines, fear of side effects, vaccine misconceptions, fear of needles, mistrust of public health institutions, and concerns about vaccine effectiveness. Complacency factors included reliance upon traditional and alternative medicines, lack of knowledge about vaccines, and minimising the seriousness of influenza illness. Convenience factors included perceived costs of the vaccine and a lack of influenza vaccine promotion. Conclusion: Addressing confidence, complacency and convenience factors is important to increase influenza vaccine acceptance and uptake in South Africa.