The late Early Pleistocene archaeological site of Fuente Nueva-3 (FN3), which lies in the Guadix-Baza Depression (SE Spain) and is dated to ~ 1.4 Ma, contributes some of the oldest evidence of hominin presence in Western Europe, including a huge tool assemblage of Oldowan tradition, manuports (i.e., unmodified stones used as percussion tools) and abundant fossils of large mammals, some of which preserve anthropogenic marks related to defleshing, butchering and marrow processing. In addition, there are bones with tooth marks produced by scavenging carnivores. The fertile layers of the FN3 section have been grouped in a lower archaeological level (LAL) and an upper archaeological level (UAL). Both levels preserve abundant skeletal remains and lithic tools. However, the LAL shows a high density of manuports, which suggests that hominin activity was more intense at this level, while the UAL preserves many remains of megaherbivores, particularly proboscideans (Mammuthus meridionalis), and almost all coprolites unearthed from the site, which points to a greater involvement of the giant hyenas (Pachycrocuta brevirostris). In this paper, we (i) test for statistical differences in the composition of the faunal assemblages preserved in the UAL and LAL; and (ii) analyze particle size in the fertile layers of both archaeological levels. Our results show that megaherbivores are comparatively overrepresented in the UAL, specially by young elephants, while other medium-to-large and large-sized ungulates, particularly equids, are more abundant in the LAL, showing a predominance of adult individuals