The recent progression of vanilla production in Indonesia has been relatively slow, although vanilla prices were relatively high. The main factors inhibiting the progress are the threat of theft of vanilla fruits and incidents of vanilla stem rot disease, especially in West Java. Three cultivation systems are found in Indonesia: conventional, shade house, and greenhouse cultivation. The last two systems were intended to address both threats. This study analyzed the sustainability ranking of the three vanilla cultivation systems. Qualitative research was conducted to find the facts on how farmers decide to apply the cultivation systems, particularly in addressing the threats to achieving sustainability. Based on the facts of the vanilla cultivation conducted by farmers, the experts analyzed to sort the most sustainable cultivation from technical, economic, and environmental aspects. The data was obtained from experienced vanilla farmers and cultivation and economic experts through in-depth interviews and direct observation of farmers’ plantations. The result showed that the use of shade houses is the most sustainable vanilla cultivation because it can provide higher productivity and quality, is relatively safe from the threats of microenvironment settings, is more affordable, and is easier to maintain and control the disease.