Background: Previous studies have shown that the controlling behaviour of physical education teachers might be detrimental to their students’ psychological experiences. The purpose of this work was to examine whether and to what extent the different dimensions of the perceived controlling teaching questionnaire predict students’ basic psychological needs, motivations, and physical activities during leisure-time. Methods: A total of 299 students (164 boys and 135 girls) from four Estonian general education schools and two vocational education institutions participated in the study. Students filled in the questionnaire of study variables. A variance-based structural model was used to test the research hypotheses. Results: The results revealed that different forms of controlling behaviours predicted psychological need frustration (β = 0.09–0.37; p
< 0.01). Psychological need frustration predicted controlled motivation (β = 0.52; p
< 0.01). Controlled motivation predicted subjective norms (β = 0.51; p
< 0.01). Intention was predicted by attitudes (β = 0.30; p
< 0.01), perceived behavioural control (β = 0.37; p
< 0.01), and subjective norms (β = 0.15; p
< 0. 01). Attitude was statistically significantly related to leisure-time physical activity (β = 0.09; p
< 0.05). The model describes 10% of students’ physical activity in the context of leisure-time. Conclusion: The results of this study highlight that physical education teachers should avoid using controlling behaviours if the aim is to avoid frustrating their students’ psychological needs, which might have detrimental effect on students’ leisure-time physical activity via controlled forms of motivation.