Pesantren (Islamic boarding school) has proven to be a formidable institution in society by ruling Islamic values and traditions, including in agricultural field. Having variety of available resources, pesantren becomes a power for agricultural development. Pesantren has transformed to be able to maintain the agricultural tradition in achieving food sustainability. This research aims to assess transformation system and formulate strategies for pesantren transformation to achieve food sustainability. This research uses soft system methodology (SSM) approach and SAST (Strategic Assumption Surfacing and Testing) technique. The result shows that pesantren transformation system uses 4R concept that is located on the reframe and renew dimensions. The strategies to encourage the pesantren transformation cycle: their lead/central figure (leadership); pesantren management to institutionalize values for both individual and collective; and having strong modalities. The anticipation for transformation obstacles includes a change that must be well managed and economic orientation for the green growth.