Background: Despite the acknowledged role of leadership in the psychosocial work environment, few studies focus on how leadership qualities and strategies may act as key processes of importance to positive effects of workplace health promotion (WHP). The aim of this study was to increase knowledge about how leadership qualities and strategies in WHP projects influence employees’ long-term work attendance. Method: The 1- and 2-year effect of leadership on the prevalence of long-term work attendance among municipal human service workers (n = 3 275) was analysed using 3-year register-based data on sick leave, questionnaires and a qualitative categorization of each unit. Result: Increased leadership qualities, especially where leaders used rewards, recognition and respect, were associated with higher prevalence of work attendance at follow-up [PR 1.42 (1.20–1.69)]. Leaders’ strategies and views on work-related health had a significant impact on increased work attendance in projects that had goals clearly focusing on changeable factors [1.36 (1.11–1.67)], in multi-focused projects [1.60 (1.24–2.04)] and in projects aimed to increase employees’ awareness of their health. Workplace health promotion strategies with a single focus on strengthening individual, professional or organizational resources were negatively associated with work attendance. A higher proportion of employee work attendance was also seen in units whose leaders viewed the organization or the society (rather than individual workers) as responsible for the high rate of sick leave. Conclusion: Leadership, WHP strategies and leaders’ attitudes towards employee work-related health have importance for implementation processes, as well as affecting employee work attendance. In this study, multi-focused WHP interventions had the largest effect on work attendance.