Habitat disturbance and particularly land-use change from natural habitats to forest plantations, croplands, and urban expansion have caused a rapid biodiversity loss in southern South America's temperate rainforests. In those forests, bryophytes constitute a crucial component, with important ecosystem roles. We evaluated bryophyte diversity and species turnover between native temperate forests and sites with different degrees of disturbance to gain insight into how habitat disturbance affects the bryophyte community. We used four different habitat disturbance scenarios at a temperate rainforest, comprising primary native forests, secondary forests, clear-cut areas, and abandoned Eucalyptus forest plantations. We sampled bryophytes for three years (2016 to 2018) on four substrates (rock, soil, live wood, and deadwood). We found that species richness decreases, and turnover increases as disturbance increases. Liverworts were more sensitive to habitat disturbance than mosses, reaching their highest diversity in primary forests. Substrate availability was also a key factor for the bryophyte community, as species were non-randomly distributed among them. In conclusion, habitat disturbance affects the temperate forest bryophyte community, altering its composition along with disturbance conditions. Considering the crucial roles that bryophytes play within the ecosystem, these changes can also affect bird and mammal species that use them as nesting material.