Adolescence and youth are crucial periods in life, during which young people undergo physical, sexual, psychological and lifestyle changes as they mature into adulthood. To better understand how adolescents and youth in Mongolia (aged 15–24 years) can be supported at this critical time of life, an ecological model was formulated to study their knowledge, attitudes and behaviours at individual, family, social and environmental levels, around healthy lifestyle, sexual and reproductive health (SRH), substance use, mental health, bullying and gender-based violence (GBV). The purpose of this research is to comprehensively understand the knowledge, attitudes, practices, drivers, bottlenecks and communication channels pertaining to the health behaviours of Mongolian adolescents and youth aged 15–24 years. This understanding will inform behaviour change communication and ultimately contribute to the adoption of positive health practices.