The study aimed to analyse changes in school belonging in higher education students during online instruction and to verify its cross-sectional and longitudinal relationships with academic adjustment in the first and higher years of study. The research sample consisted of 169 higher education students (90.5% women, M = 21.71; SD = 2.63) in the first measurement (end of the winter term), and 77 respondents (96% women, M = 21.38; SD = 2.03) in the second measurement (end of the summer term). Self-report methods were used. Results showed a decline in school belonging among first-year students. School belonging significantly predicted academic adjustment, and the relationship with internal motivation persisted even four months later. The findings support the key role and need for facilitating school belonging in higher education students in the online environment.