Meditation is a popular mind-body practice with numerous benefits, but its neural mechanism remains unclear. Previous MRI studies have shown morphometric changes associated with meditation, such as increased grey matter volume (GMV). However, these findings were in adults and adolescents remained understudied. Using voxel-based morphometry, we assessed GMV changes in adolescents participating in a training containing elements from mindfulness meditation and yoga-based practices. We found a significant GMV decrease in the left posterior insula, a key homeostatic awareness and interoception region. The decreasing GMV opposes previous findings of structural increase in adults, which may be due to adolescence-specific developmental processes.