The coronavirus disease 2019 (COVID-19) pandemic resulted in restrictive measures like home-confinement in many countries. In Spain, outdoor leisure activities were banned for nearly two months and then, going out became gradually allowed. Previous studies reported that physical activity (PA) levels decreased due to the confinement in several countries where restrictions were applied. However, it is not known whether the effects of the confinement remained after finishing it. The aim of this study was to analyse the changes in physical activity in Spanish university students before, during and after the confinement by COVID-19. We also analysed enjoyment with physical activity and the tools used. An online questionnaire, which included the International Physical Activity Questionnaire – Short Form and information regarding PA preferences was designed and distributed during (April 16^th-May 2^nd) and after (July 15^th-August 31^st) the confinement. 2,524 participants filled in both surveys. Levels of moderate-to-vigorous PA were higher after than during the confinement (p<0.01). However, it did not reach pre-confinement levels (p<0.0001). Time spent on strength and high intensity interval training decreased after regarding pre-confinement levels (p<0.0001, both). Participants enjoyed more doing PA after than before and during the confinement. Social networks, equipment for aerobic and strength exercise were tools less used after than during confinement (p<0.0001, p<0.0001, p<0.0001; respectively). However, their use remained higher than before (p<0.0001, p<0.0001, p<0.0001; respectively); while gyms were less used (p<0.0001) after the confinement. These data demonstrate that COVID-19 pandemic and its related measures have impacted on PA of university students, with the potential to affect healthy habits that could be maintained throughout life. Considering that currently there are restrictions to practice PA, it is important to promote it among university students to recover and even enhance pre-confinement levels.