A remarkably long period of Northern Hemispheric cooling in the 6th century CE, which disrupted human societies across large parts of the globe, has been attributed to volcanic forcing of climate. A major tropical eruption in 540 CE is thought to have played a key role, but there is no consensus about the source volcano to date. Here, we present evidence for El Chichón in southern Mexico as the most likely candidate, based on a refined reconstruction of the volcano’s eruption history. A new chronological framework, derived from distal tephra deposits and the world’s largest Holocene beach ridge plain along the Gulf of Mexico, enabled us to positively link a major explosive event to a prominent volcanic sulfur spike in bipolar ice core records, dated at 540 CE. We speculate that voluminous tephra fall from the eruption had a severe environmental impact on Maya societies, leading to temporary cultural decline, site abandonment, and migration within the core area of Maya civilization.