Biological soil crusts (biocrusts) composed of cyanobacteria, bacteria, algae, fungi, lichens, and bryophytes stabilize the soil surface. This effect has mainly been studied in arid climates, where biocrusts constitute the main biological agent to stabilize and connect soil aggregates. Besides, biocrusts are an integral part of the soil surface under Mediterranean and humid climate conditions, mainly covering open spaces in forests and on denuded lands. They often develop after vegetation disturbances, when their ability to compete with vascular plants increases, acting as pioneer communities and affecting the stability of soil aggregates. To better understand how biocrusts mediate changes in soil aggregate stability under different climate conditions, we analyzed soil aggregate samples collected under biocrust communities from four national parks in Chile along a large climatic gradient ranging from (north to south) arid (Pan de Azúcar, PA), semi-arid (Santa Gracia, SG), Mediterranean (La Campana, LC) to humid (Nahuelbuta, NA). Biocrust communities showed a stabilizing effect on the soil aggregates in dry fractions for the three northern sites and the wet aggregates for the southernmost site. Here, permanent vascular plants and higher contents of organic carbon and nitrogen in the soil control aggregate stability more than biocrusts, which are in intense competition with higher plant communities. Moreover, we found an increase in stability for aggregate size classes < 2.0 and 9.5–30.0 mm. The geometric mean diameter of the soil aggregates showed a clear effect due to the climatic gradient, indicating that the aggregate stability presents a log-normal instead of a normal distribution, with a trend of low change between aggregate size fractions. Based on our results, we assume that biocrusts affect the soil structure in all climates. Their role in aggregate stability is masked under humid conditions by higher vegetation and organic matter contents in the topsoil.