We investigated the effects of My Teaching Partner—Secondary (MTP-S), a teacher professional development intervention, on students’ peer relationships in middle and high school classrooms. MTP-S targets increasing teachers’ positive interactions with students and sensitive instructional practices and has demonstrated improvements in students’ academic achievement and motivation. The current study tested the prediction from systems theory that effects of MTP-S on students would extend beyond the academic domain—that is, the ecology of teachers’ behaviors towards students should also influence the ecology of students’ behaviors towards one another. Participants were 88 teachers (43 randomly assigned to MTP-S and 45 assigned to a control group that received the regular professional development offerings in their school) and 1423 students in their classrooms. Observations and student self-report of classroom peer interactions were collected at the start and at the end of the course. Results indicated that in MTP-S classrooms, students were observed to show improvement in positive peer interactions, although this pattern was not found in self-report data. However, moderation analyses suggested that for students with high disruptive behavior at the start of the course, teacher participation in MTP-S mitigated a typical decline towards poorer self-reported peer relationships. The relevance of findings for the social ecology of classrooms is discussed.