We present a paleoenvironmental and paleoclimatic reconstruction based on microfaunal assemblages preserved at Lezetxiki II Cave (Arrasate, Basque Country, Iberian Peninsula) and synthesize previously published and new chronological work from the cave to better understand the environmental history of the region. The stratigraphic sequence of this short gallery ranges from the end of the middle Pleistocene to the middle Holocene and has great micropaleontological relevance for the Iberian Peninsula, especially because it contains the most ancient small vertebrate remains found in the Cantabrian region, likely deposited during Marine Oxygen Isotope Stage 7–6. Thirty-two small vertebrate taxa, including two extinct species, were identified. Environmental reconstruction based on small vertebrates suggests an open landscape at the base of the sequence (three lower levels) that progressively changed to woodland in the upper levels. Other paleoenvironmental data suggest a similar interpretation of the environmental history of the region, and although some uncertainty in the environmental reconstruction and chronology still exists, our data provide a richly detailed record of small vertebrates from an area that likely represented an important late Quaternary migration corridor for species traveling between the Iberian Peninsula and European continent.