In software engineering capstone projects, students collaborate in teams to deliver software solutions to real clients. This is often the first experience for many students in which they must collaborate, explore new technologies, navigate ambiguous requirements, and balance project demands alongside other academic responsibilities. These overlapping demands often lead to emotional strain. While prior research shows that emotions affect learning and motivation, most studies have focused on short-term, individual programming tasks rather than long-term, real-world projects. This study investigates the emotions students experience during a capstone project and explores the triggers associated with these emotional responses across project stages. We conducted a thematic analysis of reflective learning diaries written by 24 students from three Scrum teams over a 14-week course. The analysis was grounded in Control-Value Theory, which explains how students’ emotional experiences are shaped by their perceived control over tasks and the value they assign to them. Frustration emerged as the most frequently experienced emotion, often triggered by technical challenges, ambiguous requirements, and coordination issues. Positive emotions such as hope, pride, and gratitude were tied to early goal setting, overcoming challenges or reflections on personal growth and support. Emotional patterns varied across project phases, revealing shifts in affective engagement over time. We also observed gender-based differences: male students more often linked frustration and shame to technical failure, while female students described anxiety, gratitude, and enjoyment in connection with team dynamics and communication. Our findings highlight the importance of designing emotionally aware capstone learning environments that support students’ psychological well-being and motivation as they navigate the affective demands of real-world software engineering.