Background: Research clearly points toward a relationship between teaching behavior and students' affect. The relations between teaching behavior and middle school students' mental health, in the form of positive and negative affect, are particularly important to understanding how school-based clinicians can provide support for teachers and students alike. However, studies examining the relationship between teaching behavior and students' positive and negative affect are largely cross-sectional and focus on high school students. Objective: Our objective was to determine the temporal directionality between instructional, negative, organizational, and socio-emotional teaching behavior and affect in middle school students. Methods: At two time points, 335 students in grades 6 to 8 (mean age: 12.59; SD = 1.01; 47.4% female) filled out the Teaching Behavior Questionnaire and the Positive and Negative Affect Scale. Results: Our two-level hierarchical linear model analyses revealed no significant associations between teaching behavior and positive affect (ps > 0.05). However, socio-emotional teaching behavior and negative affect were positively and bidirectionally associated (ps < 0.01). Further, negative teaching behavior (p < 0.01) was positively associated with later negative affect and negative affect was negatively associated with later instructional teaching behavior (p < 0.01). Conclusions: Our findings highlight the differences in the existence and temporal directionality of associations between the different types of teaching behavior and students' positive and negative affect. In particular, different types of teaching behavior are only associated with students' negative but not positive affect. Experimental studies with students from more diverse ethnical and racial background are needed.