Research suggests that the relation between student-teacher conflict and children’s externalizing behavior might be reciprocal, and possibly also between student-teacher conflict and children’s social skills. Because children with externalizing behavior also tend to display low levels of social skills, we do not know if one or both of these student characteristics are involved in shaping and being shaped by the relationship to the teacher. In this study, we addressed this by means of a three-wave cross-lagged longitudinal study from preschool to third grade, including measures of social skills, externalizing behavior and student-teacher conflict. Bidirectional relations were observed between student-teacher conflict and social skills from first grade to third grade, and between student-teacher conflict and externalizing behavior between preschool and first grade. However, results from a model including both social skills and externalizing behavior suggested that externalizing behavior is a stronger predictor of conflicted student-teacher relationship than children’s social skills. Student-teacher conflict was predictive of externalizing behavior as well as of later social skills. Effect of children’s first-grade externalizing behavior on third-grade student-teacher conflict was gender moderated, with stronger effects of externalizing behavior observed in girls, combined with higher stability in first-grade student-teacher conflict in boys.