Summary1. Seed dispersal is thought to be unpredictable and outside a plant's control. But directed seed dispersal by mutualistic birds can increase probabilities of germination and survival by the non-random deposition of seeds in suitable microhabitats. 2. In the Sonoran Desert grasslands of southern Arizona (USA), bird-dispersed wild chiltepin peppers (Capscium annuum var. glabriusculum) grow in non-random association under bird-dispersed nurse trees and shrubs that serve as perches. We tested the hypothesis that the pattern is maintained by directional avian seed-dispersal patterns. Alternatively, post-dispersal processes, such as differential seed predation and seedling mortality, could create the associations. 3. For 3 years, we sampled the bird-generated seed rain under desert trees in four chiltepin subpopulations, comparing seed dispersal into microhabitats of fleshy-fruited trees and non-fleshy-fruited trees. Celtis pallida (fleshy-fruited) and Prosopis vellutina (non-fleshy-fruited) trees accounted for > 90% of the cover available for chiltepin recruitment. We tracked seedling emergence and survival in the two microhabitats and conducted a controlled seed-addition experiment to measure the effects of microhabitat, seed-addition density and temporal seed deposition on chiltepin emergence, growth and survival. 4. Approximately twice as many bird-dispersed seeds arrived at fleshy-fruited microhabitats compared with non-fleshy microhabitats. The numbers of seeds arriving and the number of seedlings emerging in microhabitats the following year were positively correlated. Survival of naturally emerged seedlings was similar at both microhabitats, but the seed-addition experiment revealed that more seeds are able to emerge under the denser foliage of fleshy-fruited microhabitats. The experiment also shows a significant effect of temporal deposition: when seeds were added gradually in a microhabitat (emulating repeated avian seed deposition under perches) instead of all at once, seedling emergence increased twofold on average. 5. Synthesis: Birds dispersed disproportionally high quantities of chiltepin seeds into favourable recruitment microhabitats, showing a case of directed dispersal. Birds also increase seedling emergence through the temporal deposition of seeds under fleshy-fruited trees, most likely as a result of reducing the odds of seed predation. A coupling between directed seed dispersal with classic facilitative plant-plant interactions leads to the formation of pattern and self-organization in a plant community.