The Lomas ecosystems are fog-dependent oases within the hyper arid band of the Peruvian coast. Biological soil crusts (BSC) formed in the Lomas interact with the fauna and flora, but relationships among these groups have not been investigated. Here we asked if natural bioperturbations made by fossorial birds that disrupt BSC cover are increasing plant diversity in the Lomas at the National Reserve of Lachay in Peru. We analyzed active and inactive avian bioperturbations and measured the soil seed bank and the field emergence of seedlings. The plant community observed in the soil seed bank showed lower abundance of seedlings in active bioperturbations than undisturbed BSC or inactive bioperturbations. However, the emergence of seedlings in the field presented a different pattern, where both active and inactive bioperturbations were richer and more abundant in seedlings than the soil with undisturbed BSC. Our results show that bioperturbations by fossorial birds have a positive effect on seed germination and supports a richer vascular plant community in a unique ecosystem of the Peruvian desert. Here we demonstrate the importance of spatial and temporal heterogeneity for ecosystem structure and functioning.