Abstract The group selection cutting system provides a promising technique for transforming monospecific even-aged stands into uneven-aged, mixed stands. However, this system has scarcely been used to regenerate Mediterranean shade-intolerant species. In this study, we analyze the height increment patterns of Pinus pinaster seedlings emerging in naturally regenerated gaps. P. pinaster is a shade-intolerant pine species distributed throughout the Mediterranean basin. An experimental trial was established in a 50-year-old P. pinaster (maritime pine) plantation located in the mountains of central Spain. Gaps of two different sizes (diameter equal to 1.5 and 2.5 times the dominant height of the stand, 26 and 44 m, respectively) were opened during winter 2017–18. A total of 531 subplots with a 1-m radius were installed in spring 2018, distributed within the gaps as well as in control plots adjacent to the gaps. Seedlings were tagged individually and variables including height, along with other ecological variables, were collected twice a year (in spring and autumn), providing six time intervals for the development of our models. We applied seemingly unrelated regression to analyze the height growth in this polycyclic species, allowing us to model spring and autumn height increments at the same time. Our results showed that seedling height growth depended on the silvicultural treatment, meteorological conditions during the spring growth season, inter-specific scrub competition, position within the gap, and seedling characteristics, such as the ontogenetic development or the size of the seedling itself. This work, along with germination and survival analysis, aims to provide a holistic perspective on the suitability of the group selection cutting system to regenerate maritime pine stands, taking into account current and future climate change scenarios.