Understanding how small mammals (SM) associate to environmental characteristics in olive groves is important to identify potential threats to agriculture and assess the overall conservation value and functioning of agro-ecosystems. Here, we provide first insights on this topic applied to NE Portugal olive groves, by assessing the landscape attributes that determine SM occurrence, focusing on one species of conservation concern (Microtus cabrerae), and one species often perceived as a potential pest of olives (M. lusitanicus). Based on SM genetic non-invasive sampling in 51 olive groves and surrounding habitats, we identified seven rodent species and one insectivore. Occupancy modelling indicated that SM were generally less detected within olive groves than at surrounding habitats. The vulnerable M. cabrerae reached a mean occupancy (95%CI) of 0.77 (0.61-0.87), while M. lusitanicus stood at 0.37 (0.24-0.52). M. cabrerae was more likely to occur in land mosaics with high density of agricultural field edges, while M. lusitanicus was more associated to high density of pastureland patches. Overall, our study suggests that spatially complex and heterogeneous olive grove agro-ecosystems may favor the occurrence of species-rich SM communities, possibly including well-established populations of species of conservation importance, while keeping potential pest species at relatively low occupancy rates.