During the Pleistocene, the Yucatán Peninsula reached its greatest geographic extension, with 457,650 km2, but the rise of sea level after the Last Glacial Maximum (ca. 20,000–12,000 years ago) reduced its area to 225,182 km2 (50.8% reduction). These geographic extension changes likely modified the extension of different habitats throughout the peninsula, which may have also promoted morphological changes in the species that inhabit this region. Here, we tested if the reduction of the geographic size of the Yucatán Peninsula may have promoted changes in the body size of three fossil bird species and two modern bird species. We compared Late Pleistocene bird fossils specimens from Loltún, Yucatán, Mexico (ca. 28,000–11,700 ya), San Josecito Cave and Tlapacoya, and study skins of collected specimens. To assess the area‐scale ratio and to establish if body size changes occurred over time from a large to a small body size, we relied on the “island rule” as a framework; we also relied on Bergmann's rule, which postulates a decreasing in size from north to south in homeothermic species to recognize if these birds show a north to south cline. Based on body mass and measurements of the tarsometatarsi, a reliable proxy for the estimation of body size, we performed statistical analyses to test for differences between fossil and non‐fossil birds, as well as to test a gradient in body mass north to south. We found a statistically significant trend in body size changes through time, from small body sizes in fossil birds to larger body sizes in non‐fossil birds. These results suggest that relatively recent ecological factors related to the environmental carrying capacity may have promoted body size variations in birds from the Yucatán Peninsula. We also found that modern population of bird species follow Bergmann's rule.