The ecological consequences of homogenization remain relatively unexplored. One example of landscape-homogenizing is the establishment of plantations. We studied the effect of human-made forests by contrasting plant and small-mammal community composition between planted tree stands and adjacent natural habitat in two different Mediterranean habitats in Israel: (1) inland habitat where we focused on pine (Pinus halepensis) and carob (Ceratonia siliqua) stands, and (2) coastal sand dune habitat where we focused on planted acacia (Acacia saligna) stands. We first wanted to verify whether planted trees modify plant species composition, and second, if and how the small-mammal community is affected by the different habitat conditions created in plantations with different canopy cover. We were especially interested in the abundance of the commensal house mouse (Mus musculus). All tree stands underwent biotic homogenization indicated by abundance of house mice coupled with lower diversity of indigenous vegetation and small-mammal abundances and diversities. Habitat structural diversity was positively related with small-mammals diversity and was lower in artificial tree stands in both habitats. Our results suggest that using the abundance of commensal generalist species such as the house mouse relative to other more specialist small-mammals is a good approach to determine ecosystem integrity. Pre-commercial thinning treatment is a potential management tool to maintain a proportion of native tree species within the canopy of planted tree stands. However, until sufficient data is available for making generalizations, the exact level of thinning necessary to reverse the homogenization processes in man-made plantations and keeping indigenous small-mammal communities diverse and less prone to invasion must be determined empirically.