This is a tricky question because economic output is tough to measure during wars: who knows what fraction of Belgium's GDP was lost during the First World War when most of the country became a battlefield. That said, there is an economic historian named Angus Maddison who has done the best work I'm aware of measuring historical economies. Here is a link to his estimates of per capita GDP through history by country. Its a really cool dataset which gives you a sense of relative standards of living in various parts of the world. Take it with a grain of salt though, who knows how accurate anything pre-1980 is. If you look through his figures for declines from pre-event peaks to post-event troughs these stood out to me (remember these are all quoted in income per capita):
The Russian Empire / The Soviet Union (1914-1921) From the start of the First World War to the end of the Russian Civil War the death toll was approximately 10 million. This is something like 10% of the Russian population at the time. The economy was completely wrecked as armies were fighting across the entirety of Russia. Not to mention that the country was cut off from world trade as a result of the formation of the USSR. GDP per capita decline: 62%
Iran (1979-1988) The Iranian revolution prompted the exodus of much of the country's economic elite and the economy contracted significantly. A year later Iraq invaded and nearly a million Iranians died fighting them through the 1980s. A decade of oil embargoes, horrible economic mismanagement, and being an international pariah later: GDP per capita decline: 49%
Congo (1990-2003) The civil society of Zaire began to unravel in 1990 and progressively fell apart over the next decade. The first Congo War (1996-1997) and Second Congo War (1998-2003) killed millions of people and laid much of Eastern Congo waste. The population grew very quickly during this period so the 62% decline in per capita GDP overstates the impact on the economy overall.
The declines recorded for Liberia and Nauru aren't nearly as steep. This doesn't surprise me too much because a 90% economic contraction is too extreme. If Liberia was barely feeding itself pre-civil war then a 90% decline in GDP would lead to mass starvation and population decline which didn't happen. Its possible that cases like these aren't measured correctly though. For example, I thought it was weird that Cambodia's Khmer Rouge period didn't see living standards fall that much in the data when it was clearly a horrific national trauma.
I'd probably go with the collapse of Mycenaean Greece. Of course I do not have % statistics for this event since it occurred in around 1100 bc. However, consider this: in 1200 BC Greece was a prosperous place divided up into city states ruled from palaces. There was a vibrant culture of Arts, Wall Painting and pottery and there was extensive trade not only between the Greek city states themselves but also with Egypt and the near east. Fast forward to 1050 B.C. and we have a very different story. The great palaces at Mycaenae, Pylos Argos and others have been overthrown and the states with them. Writing has disappeared completely and would only be reintroduced by the Phonecians centuries later. Trade also has dried up and the sophistication of goods produced (such as pottery) was much lower, indicating that labour was less specialised. Population declines significantly and does not recover for centuries. However, the most telling way to measure the severe contraction of Greece is the time that it took for the region to recover economically to what it had been in 1100 B.C. Greece only emerged from it's dark age in about 800 B.C. it took the region 300-400 years to recover from the Bronze age collapse.
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