SAN PEDRO SULA, Honduras—The coffee equation in Central America has changed.

This year, Honduras passed Guatemala as the top coffee producer in Central America, the region that produces the bulk of the world's washed arabicas, the most expensive and sought-after coffee beans, which are used in gourmet blends. Honduras's harvest this season was 3.8 million 60-kilogram bags of coffee, compared with 3.5 million bags for Guatemala.

While...