This study investigated the development of study engagement from the end of upper secondary school through the first and second years of higher education. The participants experienced the challenges related to the first wave of the COVID-19 pandemic while they were either university students or preparing for university entrance exams. The study employed a person-oriented approach to determine what kind of developmental trajectories emerge in study engagement when following the student participants from the end of upper secondary school through the first and second years of higher education. Furthermore, the study investigated whether socio-emotional skills obtained by the end of secondary school and before the pandemic play a role in more adaptive development through demanding restrictions related to the worldwide pandemic and general changes in the learning environment. The 852 participants answered questionnaires on study engagement and socio-emotional skills in spring 2019, and of them, 426 individuals who continued their education answered regarding study engagement again in spring 2020 and winter 2020/2021. The grades in math and Finnish language were also included. The results indicated that most students tended to experience a drop in study engagement during the first wave of COVID-19 compared to the pre-pandemic level; however, they managed to boost their engagement back to previous levels approximately 6 months later. Students who managed to recover their engagement also tended to have higher socio-emotional skills than students who were struggling with study engagement before the pandemic or who started to struggle during the pandemic.