This study explores the social integration of Ukrainian refugee students in Czech schools, focusing on peer network dynamics in classrooms with a significant proportion of ethnic minority students. We employ longitudinal social network analysis combined with qualitative insights to investigate the evolution of friendship and exclusion ties among 266 students (ages 11–15, 45.11% girls, 21.05% Ukrainian) in 12 classrooms across two time points during the 2022/2023 school year. Our study introduced socioeconomic status (SES) and sociocultural adaptation as key explanatory variables, hypothesizing their roles in fostering cross-ethnic interactions. Overall, we found that ethnic homophily decreased over time, indicating greater cross-ethnic mixing, even as overall number of friendships in classrooms declined. Ukrainian students were initially less integrated into peer networks, exhibiting fewer friendships and strong preferences for intra-ethnic ties. However, this disparity became less pronounced as the school year progressed. Sociocultural adaptation emerged as a significant predictor, with adapted Ukrainian students more likely to receive friendship ties and less likely to receive exclusion ties, highlighting the critical role of pro-social behavior in social integration. Conversely, SES did not significantly affect the formation of cross-ethnic ties. These findings underscore the dynamic nature of peer relationships and the importance of fostering sociocultural adaptation to support refugee students' integration. We discuss implications for educational policies aimed at promoting inclusive school environments and propose directions for future research on intergroup dynamics in diverse classrooms.