Student's motivation towards physical education (PE) classes is a key factor for increasing physical activity (PA) levels in children. In order to increase motivation in PE, new teaching techniques are needed, such as gamification. This study examines the potential influence of gamification in PE classes on motivation-related variables such as basic psychological needs (BPNs) and positive behaviours in primary school students, considering the perceptions of students and teachers. A total of nine teachers and 506 primary students participated in this study: 250 from a gamified group and 256 from a control group. The students filled in the BPNs in the Classroom Scale in order to measure three BPNs (autonomy, competence and relatedness). In addition, the perceptions, feelings, and behaviours of the students and teachers were analysed and classified through drawings, teacher's diaries, and focus groups. An improvement in the three BPNs, namely autonomy (p < 0.001), competence (p < 0.001) and relatedness (p < 0.001), was observed for the gamified group compared to the control group. The qualitative findings showed a perceived increase in student motivation, participation, and cooperation behaviours. Students also reported values such as respect, and rejection of contempt and harassment. In short, gamification was associated with an increase in all BPNs and positive behaviours in primary school students in gamified PE classes compared to non-gamified classes.