The Philippines' weather bureau already expects rainfall to be "way below" normal by April in most parts of the country, including rice-growing provinces in the Central Luzon region and sugar plantations in the Visayas provinces. El Nino could worsen that.
Previous El Nino episodes caused severe dry spells in the archipelago affecting vast tracts of farmland. A rice shortfall due to typhoons and drought connected to El Nino in 2010 prompted record imports of the national staple.
Global cocoa prices jumped to their strongest in more than two years in February on concerns a returning El Nino could cut output in main producers Ivory Coast, Ghana and Indonesia. The global market is expected to experience a second straight deficit in 2014.
Erratic weather could affect the development of coffee cherries and cocoa pods. In Indonesia, the world's third-largest cocoa producer, El Nino usually means extremely dry weather.
Indonesia's coffee output is forecast to fall to 9.5 million 60-kg bags in 2013/14 from 10.5 million in 2012/13 after dry weather at the start of the season reduced flowering and excessive rain during cherry development cut yields, according to the U.S. Department of Agriculture.
The Central Highlands region, which produces about 80 percent of Vietnam's coffee, has entered the dry season, and falling waters in rivers and streams coupled with strong wind would raise the risk of water shortages, according to the Science and Technology Department in the central highland province of Kontum.
El Nino usually brings warmer winters to Brazil, the world's top coffee producer, reducing the risk of coffee frost. But heavy rains would crimp production.
Drier weather could also help beat back moisture-loving roya or leaf rust fungus that is ravaging coffee plantations in Central America.
In 2009, El Nino turned Indian monsoon patchy, leading to the worst drought in nearly four decades which helped push global sugar prices to their highest in around 30 years.