The recent Regulation (EU) 2019/1381, published on the 6th September 2019, aims to improve the transparency and sustainability of the EU risk assessment in the food chain by amending the General Food Law Regulation (EC 178/2002) and a number of other regulations related to the food sector. This Regulation is introduced as a response to the Fitness Check of the General Food Law Regulation as well as a response to public concerns expressed by a European Citizens’ Initiative on glyphosate and pesticides. This article evaluates the amendments introduced by Regulation 2019/1381with respect to the institutional and regulatory environment in the food chain and more specifically concerning the risk assessment procedure. For this purpose, we perform a comparison of the institutional and organizational characteristics of the European Food Safety Authority (EFSA) and European Medicines Agency (EMA) in relation to the processes of risk assessment and risk evaluation, especially the processes surrounding genetically modified foods and pesticides, and how these characteristics affect the politicization of these processes. We conclude that the risk assessment process followed by EFSA would have benefitted and become more effective and less politicized, if the recent Regulation 2019/1381 had introduced some of EMA’s institutional structures and methods on risk evaluation.