Germination and seedling establishment are two critical processes in the life cycle of plants. Seeds and seedlings must pass through a series of abiotic and biotic filters in order to recruit as members of their communities. These processes are part of the regeneration niche of the species. In arid regions, the regeneration niche is frequently associated to facilitation by shade. Facilitation is a positive interaction between plants, in which one of them acts as a benefactor (the nurse) of the other (the beneficiary). The result of this interaction can be reflected in the increased growth, survival, and/or reproduction of the beneficiary plant. In this study, we determined experimentally the effect of shade and irrigation on the germination and early survival of dominant species of a semi-arid Andean region, the Bolivian Prepuna. An experiment with Acacia feddeana, Prosopis ferox, Cercidium andicola (woody species), Parodia maassii, and Oreocereus celsianus (cactus species) was carried out at an experimental garden in La Paz, Bolivia, with a bifactorial design, considering shaded and unshaded pots, subjected to two irrigation treatments (≈50 and 80 mm of rainfall during the whole study period). Microenvironmental conditions did not affect the seed germination of the woody species. However, they showed differences in seedling survival: A. feddeana survived better under shade, whereas P. ferox and C. andicola survived better without shade. Cercidium andicola, compared to P. ferox, was more affected by shade and low irrigation. Although germination success of cacti was low, both species germinated better under shade and with high irrigation. These results showed differences in the regeneration niche of dominant species of the Prepuna which may favor their coexistence and which may be characteristic of other dry Andean regions.