ANKETRAKABE, Madagascar—After a bumpy two-hour truck ride and a river crossing by canoe, Tim McCollum reached this village set beside a canopy of cacao trees, the first link in a supply chain that would help boost production at his small African chocolate factory.

The good news was that Mr. McCollum's Madécasse Chocolate LLC. had located a rare source of premium cocoa before another competitor. That was also the bad news.

Mr. McCollum learned villagers had zero experience dealing with global customers—one 71-year-old told him he was the first white man he'd seen here since Madagascar gained independence from the French in 1960. Then there was the river. Nobody on his team was sure how to move a ton of cocoa across it in a canoe. But after meeting with the local farming cooperative, Mr. McCollum became convinced that cocoa grown here could make the 600-mile journey to his factory and be shipped to U.S. supermarkets from Madagascar, an island off Africa's southeast coast.