<p>Within Self-Determination Theory’s theoretical framework, student motivation is considered a crucial factor for school success and well-being, related to the capacity of the learning environment to meet individuals’ psychological needs. The purpose of the present study was to analyze the longitudinal trajectories and associations of students’ lack of autonomous motivation (amotivation) and a specific feature of the learning environment, students’ perceptions of teacher justice, over the course of one school year, and the concrete teacher practices associated with this feature. Students in 9th to 13th grade (<i>M</i>_age = 16.28, SD_age = 1.57, 69% male, 90% born in Italy) completed a self-report questionnaire in three waves over one school year (<i>N</i> = 787 in T1, 772 in T2, 836 in T3). Latent growth curve models (LGCM) were estimated to test individual trajectories and the interaction between motivation and teacher justice as parallel processes. The models indicated an increasing trajectory for both amotivation and perceptions of teacher justice, with a significant negative association among them. Increase in students’ perceptions of teacher justice were predicted by teachers’ support, clarity of assessment criteria and equity in the distribution of resources. Results highlight the importance of focusing on teacher justice as a crucial feature of the learning environment both from a theoretical perspective and for practical intervention in school.</p>