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Despite national emphasis on integrating engineering and computational modeling into science classes (NGSS Lead States, 2011), little research has investigated student perceptions of learning science through integrated projects in formal contexts. This study explores how elementary students perceive learning through an integrated project using a positive youth development lens. To understand student perspectives, three focus group interviews were conducted. Results revealed that students perceived increased autonomy and reported preferences to learning through an integrated project rather than traditional science learning. However, students believed it difficult to practice authentic science in their classroom and did not believe themselves capable of being scientists. These results can inform future research on student perceptions in integrated engineering and computational modeling approaches in science classrooms.