Vietnam has favoured the adoption of geographical indication (GI) schemes since 2001. Opportunities have opened up to the Vietnamese GIs thanks to a number of multilateral and bilateral free trade agreements coming into effect, increasing demand for certified products. However, challenges still face those involve in the GI process, especially the post-registration phase. Indeed, there is a number of unused GIs and ineffective GIs, thus not bringing any benefit to farmers. This can be explained by the fact that far from being initiated by local producers and farmers, GI process has been led by “top-down” approach of state authorities. The “top-down approach” has conducted to inappropriate selection of products to be protected initially motivated by political and commercial considerations. We recommend appropriate selection of GIs based on two important factors: specificity of the product and motivation of the stakeholders of the value chain. In view of sustainability of the food system, the GI scheme is expected to embed an improved management model, an operational control system and a comprehensive educational and awareness raising plan targeted all value chain actors and consumers.