This paper analyzes the experience of the Salvadoran cooperative movement in pursuing a political project for the institutionalization of agroecology in the years 2008–2018, under two consecutive FMLN governments in 2009 and 2014. Following El Salvador’s “turn to the left”, Salvadoran agrarian reform cooperatives and civil society allies began to allocate organizational resources toward writing public policy measures to incorporate agroecology under the FMLN government’s agricultural social program, the Family Agriculture Plan (PAF). While the cooperative sector took part in active negotiations with the FMLN party for the institutionalization of favorable policies, the former guerrilla party formulized strategies for gaining a multiclass electorate in order to remain in power. With the intention to better understand the attitude and distinct Salvadoran actors, we utilize an anthropology of public policy framework to indicate how expectations of political party legitimacy failed to shape the institutionalization of agroecology in El Salvador. We suggest that the pursuit of agroecological policies is a balancing act of making use of the State to strengthen on the ground efforts without forging organizational disarticulation following changes in government administrations.