Nature experiences, both direct and indirect, significantly impact children’s psychological well-being. However, restrictions on children’s ability to spontaneously explore nearby nature at home have been reduced. Hence, it is vital to reconnect children with nature through biophilic design at school to improve their psychological well-being since they spend most of their time there. This study aims to investigate children’s preferences towards biophilic elements and the impact of the elements on their well-being. This study involved twelve children aged 10 to 11 from two primary schools (sustainable schools) in the Northern Region of Malaysia, particularly in Kedah and Perlis. A qualitative approach, specifically phenomenology, using observation, focus groups, and projection methods, was used for data collection. The findings indicate that children preferred the implementation of biophilic elements in both indoor and outdoor learning spaces. All biophilic design elements have contributed to children’s positive emotions. However, few children exhibited negative affiliations towards water elements and plants. Overall, this study highlights the importance of embracing and implementing biophilic elements through direct and indirect experiences in indoor and outdoor learning spaces at school to improve children’s psychological well-being, subsequently contributing to their attention to learning.