Background Current efforts to motivate primary health workers in Nigeria focus on better financial incentives, and the role of other motivating factors has received less attention. The aim of this study is to explore individual and organizational determinants, their interactions and effects on motivation. Methods Exploratory qualitative research, involving semi‐structured interviews with 29 primary health workers (doctors, nurses, midwives and community health workers), was conducted in Nasarawa and Ondo states in Nigeria. Nine key informant interviews were conducted with government officials. Interviews were digitally recorded, transcribed and coded. Thematic analysis was conducted to identify common themes, as well as unique narratives. Results Results from this study suggest that health workers are motivated by individual (vocation, religion, humanity and self‐efficacy) and organizational (monetary incentives, good working environment) factors and community recognition. Supervision and leadership provided by the officer in charge as compared with that by external agencies appeared to have a positive effect on motivation. Conclusions Policy makers and donor agencies should take into account a broader range of factors while designing strategies to motivate the health workforce. The study also underscores how officer in charges with enhanced skills are likely to motivate health workers by creating a more supportive environment.