Background Habits are obtained as a consequence of cue-contingent behavioural repetition. Context cues stimulate strong habits without an individual contemplating that action has been initiated. Because of its health-enhancing effects, making physical activity a part of one’s life is essential. This study examined the associations of physical activity (PA) behaviours with PA habits and the role of autonomous motivation in developing PA habits. Methods This study used a cross-sectional design. A structured questionnaire was implemented through emails to 226 university students, where PA levels, habits and autonomous motivation were self-reported. Results Binary logistic regression identified age groups, gender and participants who were trying to lose weight as the significant predictors in meeting physical activity guidelines. Path analysis showed that moderate-intensity physical activity (β = 0.045, CI = 0.069–0.248) and strength training exercises (β = 0.133, CI = 0.148–0.674) were significantly associated with PA habits (p < 0.01). Autonomous motivation was directly associated with PA habits (β = 0.062, CI = [0.295–0.541], p < 0.01) and was also significantly related to moderate-intensity physical activity (β = 0.243, CI = [0.078–0.266], p < 0.01) and strength training exercises (β = 0.202, CI = [0.033–0.594], p < 0.05). Conclusions The emphasis on experiment-based logic and interest in habit formation in the research community is extensive. As the college years offer an excellent opportunity to establish healthy behavioural interventions, encouraging students in regular PA and exhibiting an autonomous motivation towards PA may be necessary.
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