While research on leadership and employee physical ill-being is burgeoning, the short- and long-term mechanisms through which leadership influences employee physical ill-being remain underexplored. This research, grounded in leadership theories and the Job Demand-Resource (JD-R) theory, examines how transformational and abusive leadership behaviors influence employee physical ill-being through two conflict-related negative motivational mechanisms (negative work–home interactions and job role conflict) and two negative affective mechanisms representing short-term (negative affect) and long-term (burnout) mechanisms. Employing a three-wave longitudinal design over 6 months (N = 234), our findings from a multilevel path analysis revealed that transformational and abusive leadership had respectful, negative and positive effects on employee physical ill-being via conflict-related negative motivational mechanisms and short- and long-term affective mechanisms. Notably, the influence of leadership behaviors on employee physical ill-being was more pronounced through the short-term affective mechanism (negative affect) than the long-term affective mechanism (burnout). Our findings provide a nuanced understanding of how leadership behaviors affect employee physical ill-being over time, shedding light on the dynamic interplay of motivational and affective pathways in this relationship.