The main aim of the study was to determine the associations of participation in organized physical activity (OPA), and the structure of weekly physical activity (PA) with meeting the PA recommendations among Polish boys and girls. The research was conducted between 2012 and 2019 in the Silesian region of Poland among 3499 secondary school students. To determine the structure of PA (school, transportation, home, recreation, vigorous moderate, and walking), the International Physical Activity Questionnaire-Long Form (IPAQ-LF) questionnaire was used. Adolescents participating in OPA showed significantly more PA ( < 0.001) than non-participating adolescents. The strongest associations were observed between participation in OPA and vigorous PA. The weekly recommendation of vigorous PA was met by 61% of the students with three or more lessons of OPA per week, 29% of students with one or two lessons of OPA per week, and 24% of students not participating in OPA. Therefore, boys and girls with no OPA are at greatest risk of health issues. Schools, sports clubs, and leisure institutions should increase the participation of adolescents in OPA, especially non-participants. Comprehensive school PA programs should especially include those forms of OPA that respect health weaknesses, individual talents for specific types of PA, and preferred types of PA among adolescents.