Background Most Aboriginal and Torres Strait Islander young people are able to promote their wellbeing by harnessing cultural, community and personal strengths despite the immense challenges of ongoing colonisation, racism and socioeconomic disadvantage. The Aboriginal and Torres Strait Islander health assessments can be an effective way of identifying previously undetected social and emotional wellbeing, and other health concerns, but have low uptake among young people and are often adult oriented. This study aimed to explore young Aboriginal and Torres Strait Islander people’s perspectives on appropriate content of Aboriginal and Torres Strait Islander health checks. Methods This qualitative study was conducted using a Dadirri Indigenist methodology, and semi-structured and focus group interviews with Aboriginal and Torres Strait Islander young people aged 12–25 years from the Inala community in south-east Queensland. We used reflexive thematic analysis to analyse interview and focus group data. Oversight was provided by a youth advisory group and the Inala Community Jury for Aboriginal and Torres Strait Islander Health Research. Results We interviewed 14 participants in three focus groups and four individual semi-structured interviews. Young people reported strength in culture, family relationships and autonomy in their daily lives. Threats to social and emotional wellbeing in the context of racism and ongoing colonisation included domestic violence, not having the words or safe space to discuss traumatic emotions, and described substance use as a response to trauma. Many were sceptical of mental health questionnaires and preferred open-ended conversations. Participants wanted health checks to start with identity and cultural connection, ask meaningful questions about mental health, food security, daily routine, and be conducted in a yarning style by trusted Aboriginal or Torres Strait Islander health workers of the same gender as the young person having the health check. Conclusions Health checks can be done in a way that leave young Aboriginal and Torres Strait Islander people feeling uncomfortable, confused, and avoidant of future health care. A shift is needed from transactional, tick-box approaches to relational, culturally safe practices. Youth-centred health checks should be co-designed and delivered by trusted Aboriginal and Torres Strait Islander health workers.