Cooking is frequently associated with a healthier diet, however few youth cooking intervention studies have used control groups or follow-ups. Additionally, although cooking is associated with better mental well-being among adolescents, this has not been examined experimentally. This randomised controlled trial investigated whether a five-day intensive holiday cooking program, followed by six weeks of weekly meal kits with Facebook support groups, affected the cooking-related outcomes, diet quality and mental well-being among adolescents, with a 12-month follow-up. Adolescents aged 12–15 years (intervention: n = 91, 60% female; control: n = 27, 78% female) completed baseline, post-intervention and 12-month follow-up anthropometric measures, and questionnaire measures of mental well-being, diet quality and cooking attitudes, self-efficacy and behaviours. The intervention group’s post-intervention outcomes improved significantly more for mental well-being, diet quality, helping make dinner, cooking self-efficacy and positive cooking attitude, however body mass index (BMI) z-scores also increased. Differences were maintained at 12 months for self-efficacy only. Group interviews showed that participants’ cooking behaviours were strongly influenced by family factors. Adolescent cooking interventions may have many short-term benefits, however cooking self-efficacy appears most responsive and stable over time. Effects on BMI need further investigation. Family factors influence whether and what adolescents cook post-intervention.