The Colombian armed conflict has been perhaps the most protracted internal conflict in modern history. It began in the 1960s with the creation of the Revolutionary Armed Forces of Colombia (FARC) and the National Liberation Army (ELN). Colombia is still far from being a country at peace, but in 2016, the government and FARC signed a peace agreement that ended the armed conflict between the largest guerrilla group in the country and the state. I use the case of Colombia’s 2016 Peace Agreement to examine the role of institutions in transitional justice by analyzing (1) how institutions contributed to the conflict; and (2) most importantly, their role in a peacebuilding context. I lean on the theoretical framework of transitional justice as structural justice. This theory assumes that state institutions which have contributed to conflict have to be restructured or replaced if they are to successfully contribute to peacebuilding during transitional justice. The theory also intends to move the traditional focus of transitional justice from being mainly criminal justice, to a more holistic-type justice that not only addresses violations of civil and political rights, but equally so, addresses violations of economic, social and cultural rights. The end result would be to ensure institutions and systems working efficiently to avoid that large groups keep being marginalized. I use the case of El Salvador to draw comparisons and lessons learned that can be useful for Colombia. This case is relevant because El Salvador went through a peace process a few decades ago, thus, it will allow for deeper understandings of the long-term goals that were to be achieved with the modification of several institutions. Additionally, the case of El Salvador is another example of structural injustices that spurred to an armed conflict framed in a left vs right ideological battle, similar to the one in Colombia.