Intraspecific variation in phenotype and ecology within a population is an important component of eco-evolutionary dynamics, that influence species longevity, community structure and ecosystem function. We studied nitrogen enrichment variability in a population of the dwarf little fruit bat Rhinophylla pumilio in association to its variation in skull shape. In the studied population (Atlantic Forest in northern Espírito Santo, Brazil), R. pumilio has been recorded to feed not only on fruits, as in most of its range, but also nectar. So far, this has not been recorded anywhere else for this species. Our results have shown support for phenotypic specialisation within this population that facilitates a nectarivorous diet in some individuals, contributing to intra-populational variation in this locality. Combining geometric morphometrics and stable isotope analysis, it was possible to show that skulls with longer rostra and more procumbent incisors were associated with nitrogen enrichment in the range of δ¹⁵N levels observed in other nectarivorous species at the same locality. Because nectar is a low-protein food item, nectarivorous bats often incorporate other protein sources into their diet (like pollen and/or insects). In the case of R. pumilio, the use of nectar is likely opportunistic for those individuals with favourable phenotypes. However, there is no evidence so far that R. pumilio is able to digest pollen or eventually incorporate insects in the diet. The nitrogen enrichment observed can be caused by physiological stress due to a protein poor diet, causing a mixed incorporation of nitrogen from internal and external sources (from diet). This scenario could be an intermediate step in the transition to a more nectarivorous diet, and the pattern of within-population phenotype-ecology association might shed light into the early stages of ecological specialization in phytophagous bats.