When archaeologists discovered thousands of medieval skeletons in a mass burial pit in east London in the 1990s, they assumed they were 14th-century victims of the Black Death or the Great Famine of 1315-17. Now they have been astonished by a more explosive explanation – a cataclysmic volcano that had erupted a century earlier, thousands of miles away in the tropics, and wrought havoc on medieval Britons.

Scientific evidence – including radiocarbon dating of the bones and geological data from across the globe – shows for the first time that mass fatalities in the 13th century were caused by one of the largest volcanic eruptions of the past 10,000 years.

Such was the size of the eruption that its sulphurous gases would have released a stratospheric aerosol veil or dry fog that blocked out sunlight, altered atmospheric circulation patterns and cooled the Earth's surface. It caused crops to wither, bringing famine, pestilence and death.

The Icelandic volcano of 2010, which spewed out ash which disrupted flights for a few days, was miniscule in comparison.

Mass deaths required capacious burial pits, as recorded in contemporary accounts. In 1258, a monk reported: "The north wind prevailed for several months… scarcely a small rare flower or shooting germ appeared, whence the hope of harvest was uncertain... Innumerable multitudes of poor people died, and their bodies were found lying all about swollen from want… Nor did those who had homes dare to harbour the sick and dying, for fear of infection… The pestilence was immense – insufferable; it attacked the poor particularly. In London alone 15,000 of the poor perished; in England and elsewhere thousands died."

There does not seem to have been any explanation at the time; it was probably assumed to be a punishment from God. London's population at the time was around 50,000, so the loss of 15,000 would have radically changed the city.

Surprisingly, perhaps, the volcano's exact location has yet to be established. Mexico, Ecuador and Indonesia are the most likely areas, according to volcanologists, who found evidence in ice cores from the northern hemisphere and Antarctic and within a thick layer of ash from Lake Malawi sediments. The ice core sulphate concentration shows that it was up to eight times higher than Indonesia's Krakatoa eruption of 1883, one of the most catastrophic in history.

Some 10,500 medieval skeletons were found at Spitalfields market, the site of the Augustinian priory and hospital of St Mary Spital, and the remains suggest there may have been as many as 18,000. The excavation between 1991 and 2007 by the Museum of London Archaeology (Mola) was the largest ever archaeological investigation in the capital. It was a member of that team, osteologist Don Walker, who discovered the link with a volcano. The findings will be revealed in Mola's report, to be published on Monday.

"That was a eureka moment," he told the Observer. "These people living in medieval London would have had no idea that this global event – one of the largest volcanic eruptions of the Holocene, which is the last 10,000 years, and certainly the largest of the last millennium – was causing the problems."

He now believes that mass burials in medieval pits across Britain and Europe might also have been caused by the same disaster.

When the skeletons were found, he said: "People immediately thought Black Death, or battle graves, but there wasn't enough evidence of injuries."

Radiocarbon dating revealed dates around 1250. "So we thought 'what could it be'?"

Delving into documentary evidence he found references in 1257-58 to "heavy rains" and "a failure of the crops; …a famine ensued… many thousand persons perished". Specific diseases of malnutrition – scurvy and rickets – were also found among some skeletons, although malnutrition would not have been the sole cause of death during famine. Many would have suffered hunger-induced diseases, such as dysentery, and diseases which are more a product of social disruption caused by famine, such as typhoid fever.

In exploring the cause of such devastation, he discovered that volcanologists had been trying to locate the site of this massive volcano. He said: "What is new is linking the cause of the deaths of so many thousands to this volcano. No-one has linked it to archaeological evidence – and specifically to these mass burial pits. Documentary evidence is not necessarily reliable, whereas now we've got physical evidence."

Volcanologist Bill McGuire, author of Waking the Giant, on how climate triggers earthquakes, tsunamis and volcanoes, said: "Volcanoes have a very long reach because they can impact climate…They don't just affect people nearby."

He cited an Icelandic eruption in 1783 which produced a sulphurous cloud that hung over Europe for nearly a year, affecting air quality and causing thousands of deaths.

The 13th-century eruption was far bigger, he said. "This was the biggest eruption in historic times. It may have brought the temperatures down by 4°c, a huge amount. Because it was somewhere in the tropics it meant that the winds of both hemispheres were able to carry these gases right across the planet. If you have a volcanic eruption at high latitudes, then the gases will stay in the northern hemisphere. But if you have an equatorial or tropical eruption that's big enough, then the sulphur gases can spread into both hemispheres and really encircle the whole planet in a sulphurous veil."

McGuire is Professor of Geophysical and Climate Hazards at University College London. Asked whether another such volcanic eruption is due, he said: "It's been pretty quiet for a while. I'm looking forward to something big." Only a volcanologist would take that view.

• This article was amended on 8 August 2012 to include material edited out of the print version for space reasons.