The stability of diversity of syntopic (inhabiting the same habitat in the same time) small mammals in commensal habitats, such as farmsteads and kitchen gardens, and, as a proxy of their diet, their isotopic niches, was investigated in Lithuania in 2019–2020. We tested whether the separation of species corresponds to the trophic guilds, whether their diets are related to possibilities of getting additional food from humans, and whether their diets are subject to seasonal trends. We analyzed diversity, dominance and distribution of hair δ13C and δ15N values. Diversity and dominance was not stable and differed according to human influence. The highest small mammal species richness occurred in commensal habitats that provided additional food. The degree of separation of species was higher in homestead habitats than in kitchen gardens, where a 1.27 to 35.97% overlap of isotopic niches was observed between pairs of species. Temporal changes in δ13C and δ15N values in the hair of the mammals were not equally expressed in different species. The isotopic overlap may depend on dietary plasticity, minimizing interspecific competition and allowing co-existence of syntopic species. Thus, small mammal trophic ecology is likely related to intensity of agricultural activities in the limited space of commensal habitats.