A sowing experiment was carried out using three endemic secondary successional species that commonly co-occur with Pinus halepensis in afforestations in southeast Spain. The experiment simulated the natural arrangement of needle litter over soil to test the litter's effect on seedling emergence and early growth of dwarf-shrubs and annual species, the main components of some European Habitats of Community Interest in Spain. Three sowing treatments were compared in a growth chamber: (1) soil without litter taken from clearings in a pine plantation (BARE); (2) intact soil and litter forming two distinct layers as in the field (PINE); and (3) soil and pine litter mixed in the laboratory (PINEMX). Seedling emergence of Diplotaxis harra and Thymus zygis were seven and two times higher, respectively, on BARE than on the pine litter treatments. Pine litter significantly decreased seedling biomass, length, and number of leaves of D. harra and T. zygis. Thymus capitatum was weakly affected by the presence of pine litter. We suggest that plant recruitment in the understory of P. halepensis is partially controlled by interference of pine litter, which might affect dynamics of the studied species. We propose that management practices counteract this negative effect by manipulating the pine litter layer to achieve successful ecological restoration and conservation of endemic-rich secondary communities in Natura 2000 sites in semiarid western Mediterranean areas.