Land use intensification imposes selective pressures that systematically change the frequency of wild population phenotypes. Growing evidence is biased towards the comparison of populations from discrete categories of land uses, ignoring the role of landscape emerging properties on the phenotype selection of wild fauna. Across the largest urban–rural gradient of the Colombian Orinoquia, we measured ecomorphological traits of 216 individuals of the flat-faced fruit-eating bat Artibeus planirostris. We did this to evaluate the scale of effect at which landscape transformation better predicts changes in phenotype and abundance of an urban-tolerant species. Forest percentage at 1.25 km was the main predictor affecting negatively bat abundance and positively its wing aspect ratio and body mass. Landscape variables affected forearm length at all spatial scales, this effect appeared to be sex-dependent, and the most important predictor, forest percentage at 0.5 km, had a negative effect on this trait. Our results indicate that landscape elements and spatial scale interact to shape ecomorphological traits and the abundance of A. planirostris. Interestingly, the scale of effect coincided at 1.25 km among all biological responses, suggesting that species’ abundance can be linked to the variation on phenotype under different environmental filters across landscape scenarios.