While the links between extreme weather events and mental health have received growing attention, little is known about how climate change impacts adolescent mental health in low- and middle-income climate-affected settings. To address this gap, we conducted a multi-method qualitative study exploring how young adolescents (YAs) aged 10–14 years experience climate-related stressors across six regions in Kenya. Guided by the resource insecurity framework, we thematically analyzed Elder focus groups, YA walk-along interviews and YA participatory mapping workshops. Our findings revealed that food, water and sanitation insecurity contribute to psychological distress, including symptoms of depression and suicidality, and heighten concerns of community violence (e.g., assault, fighting). Water insecurity, particularly the time and distance required for collection, disrupted school attendance, while resource borrowing generated feelings of shame. Food insecurity and larger contexts of poverty were associated with substance use as a coping mechanism, which in turn contributed to school dropout, crime and gang involvement. Poverty also led some youth to run away from home. These findings highlight the urgent need for climate-informed mental health interventions that address co-occurring resource insecurities. To advance adolescent mental health and well-being in climate-affected settings, policy responses must be targeted and multilevel, engaging families, communities and institutions.