This paper addresses the imbrications of Tunisia’s agricultural sector within neo-colonial relations of power entailing the subordination of local legal frameworks to European legislation and bodies of knowledge. It attempts to explain the reasons behind the persistent failures of Tunisia’s food security strategy through the study of the political economy of the management of plants and genetic resources for food and agriculture. Despite the 2008 food crisis and the increasing prevalence of movements and states adopting the framework of food sovereignty, the Tunisian government has failed to acknowledge or address the roots causes of food dependency. This paper demonstrates how free trade agreements with the EU function to reproduce colonial hierarchies in relations between Tunisia and European states, reducing the country’s policy space and constructing impediments to designing nationalist oriented seed laws. The Tunisian government could look to inspiration from other Global South states, which have adopted sui generis laws and treaties that protect farmers, biodiversity, and local forms of agricultural knowledge production. It analyses the factors and policies that led to the fragmentation of the institutional framework for plant genetic resources, and their role in isolating local seeds and varieties, marginalizing farmer’s traditional knowledge and undermining research and development. In addition to neoliberal reforms, this fragmentation enables the further intervention and domination of external actors and corporations. In the context of negotiations for the new EU-Tunisia free trade agreement (DCFTA), this paper argues for the urgency of rethinking a broader vision for food sovereignty outside the Global North capitalist, colonial-modern paradigm. This would require laws and institutions more in line with the country’s needs, putting local seeds and the invaluable knowledge of small farmers at the heart of policies aiming to regain sovereignty over plant genetic resources and reduce the country’s dependency.