Although Colombia has the potential to be a cocoa producer for fine flavor and high value markets, it is not greatly recognized as such. In spite of the government’s interest to position the country as a major specialty cocoa producer, no strategic actions have been taken to develop and strengthen this aspect of the value chain. This study structured a technology roadmap for the sector that identifies major research and development investment opportunities by examining the current challenges and weaknesses in key dimensions of the sector (e.g., postharvest technology, quality, capacity, and markets) that impinge on quality and add value to the product. These challenges are identified through a multidimensional and region-specific gap analysis that integrates the advances and technological trends developed worldwide as ideal practice scenarios. The findings of this study should help in prioritizing the investment of public and private resources in the sector in order to better position Colombia in the global specialty cocoa market.