Continuous warnings on quality and food safety of shrimp products from importers have led to increases in port rejections. This has increased awareness amongst Vietnamese farmers for conducting shrimp farming according to specific certification guidelines. The purpose of this paper is to clarify the situation of quality control and effectiveness of Good Aquaculture Practices (GAP) in Vietnam (VietGAP) for intensive shrimp systems by making a comparison between VietGAP and non-GAP applied farms. The farmers in the GAP system performed well on seven control points related to quality management, especially regarding reservoir construction, water monitoring, and chemical use. Of the farms, 49% reported disease, and the ratio of safety rejections was low. The farmers in non-GAP farms appeared to have weak practices in quality control with high usage of antibiotics, leading to 64% of farmers reporting disease and 20% of tested shipments being rejected. The VietGAP applied system has the potential to deal with disease and quality problems to increase export opportunity for Vannamei shrimp. However, VietGAP does not generate a high price premium in itself because it is not a recognized certificate in the global markets. The results reinforce previous findings regarding eco-certification and how it can be a useful tool to reduce small-scale producers’ risk, even though it does not necessarily generate a price premium.