Tree shelters in Mediterranean environments have a two-sided effect. They not only protect seedlings from browsing but also ameliorate microclimatic conditions, improving post-planting survival and growth. However, the ecophysiological basis of these effects are poorly understood. A factorial experiment combining light transmissivity and shelter type (solid tube vs. mesh wall) was carried out to assess the impact of contrasting microclimatic characteristics on seedling performance and physiological stress levels of shelters in two Mediterranean shrubland species (Quercus coccifera and Rhamnus lycioides) planted in a semiarid site. Even though seedlings in solid tube shelters experienced higher temperature and were slightly more photoinhibited, they had higher predawn water potential and, in general, better survival and growth than in mesh wall shelters. However, these effects were species-specific, with Rh. lycioides more favoured by solid wall shelters than Q. coccifera. However, root growth cannot explain these interactions between species and shelter type on seedling survival. Since light transmission had a marginal effect compared with wall type, we proposed that the observed effects and interaction with species are not dependent on light intensity or temperature but on other microclimatic differences like air velocity or light quality and distribution. Further studies should assess the importance of these factors on post-planting growth and physiological stress levels, which can be critical for matching the correct tree shelters type for each species in plantations in semiarid environments.