Habitat loss, fragmentation, and degradation of habitats are among the most pervasive impacts on species persistence. Mammals may vary in their response to these impacts, both in abundance and in physiological parameters. Herein, we verified how habitat quality influenced the small mammal nutritional status and stress levels among five semi‐deciduous forest remnants in the Brazilian Cerrado. To assess species' physiological responses, we used body condition as an indicator of nutritional status and neutrophil/lymphocyte (N/L) ratio as an indicator of chronic stress in Gracilinanus agilis and Rhipidomys macrurus. We sampled 264 animals belonging to the following species: G. agilis, Didelphis albiventris, Akodon montensis, Oligoryzomys spp., Rattus rattus, R. macrurus, Oecomys cleberi, Hylaeamys megacephalus, and three unidentified rodent species. We found no negative effect of reduced habitat quality on the body condition of G. agilis and R. macrurus, however, the N/L ratios of these species were lower only in high‐quality habitats, demonstrating that this parameter is an accurate indicator of chronic stress. Based on preliminary analysis, we also reported an impoverished fauna, mainly dominated by generalist species, in low‐quality habitats. Thus, we conclude that short‐term reduction in habitat quality leads to increased stress levels, which can in turn lead to future population declines and culminate in biotic homogenization. [ABSTRACT FROM AUTHOR]