Cocoa certification aims to address commodity-driven deforestation and promote sustainable agriculture, but its effectiveness remains insufficiently studied. In this study, we selected 40 cocoa plantations through stratified random sampling in Luwu Utara, Sulawesi, Indonesia, the largest cocoa producer in Asia. We assessed the implementation of cocoa certification and the vegetation structure of these plantations. Our findings show that 13 of the 40 plantations were certified under the Rainforest Alliance. Certification was primarily achieved by farmers at lower elevations, near infrastructure such as roads and cocoa collection centers, and by members of farmer associations. Consequently, certification mainly covered older plantations with less shade tree species richness, located farther from primary forest fronts. Therefore, it is too late to prevent commodity-driven deforestation. When matching certified and non-certified plantations based on elevation, we found no significant differences in shade tree basal area or shade tree species richness between them. The Rainforest Alliance requires 15% natural vegetation cover for cocoa plantations, which is too low to effectively support biodiversity or incentivize planting shade trees.