Food systems analysis is increasingly being applied to understand relations between production, distribution, and consumption of food products, the drivers that influence the system, and the outcomes that show how well the food system performs on health and nutrition, on environmental sustainability, and on income and inclusiveness. Little attention has gone to the position of global export commodities, where production and consumption are far apart. Banana in Costa Rica and cocoa in Cote d’Ivoire were the subject of this study to find out what major drivers determine the functioning of these systems. Next to identifying drivers such as population growth and increased plant disease pressure, it was found that the typical far-away setting and different living conditions between producer and consumer countries required a special eye on governance as a tripartite arena (government, private sector, civil society) with their power relations, and on certification schemes as a driver that follows from corporate social responsibility. The certification schemes addressed cover all food system outcomes, although health and nutrition in a less conspicuous way. The descriptions of the functioning of the schemes were also linked to living wages and incomes for banana plantation workers in Costa Rica and cocoa smallholder farmers in Côte d’Ivoire. Although very meaningful, certification schemes so far do not prove to be a silver bullet, but they do have the potential, in combination with other measures, to help positive food system transformations.