The transition to sustainability in agriculture faces significant challenges, especially to balance environmental goals with the practical demands of food production. This paper examines two different case studies that reveal the complexities of agricultural regulation. The first case focuses on the valorization of agri-food residual biomasses, highlighting the potential to transform food waste into valuable bioproducts such as bioenergy and biofertilizers. Despite the clear environmental and economic benefits, the absence of specific European regulations hinders the widespread adoption of these practices. Without clear rules for achieving “end-of-waste” status, the development and marketing of bio-based products remain restricted. The second case study examines the European Union’s unsuccessful effort to implement the Sustainable Use of Pesticides Regulation (SUR), which aimed to reduce pesticide use by 50% by 2030. Although the regulation sought to align agricultural practices with the EU’s Green Deal, it triggered widespread protests from farmers concerned about the potential economic losses and decreased productivity. These two cases, one showing under-regulation and the other over-regulation, highlight the need for balanced and practical regulatory frameworks that promote sustainability without imposing unrealistic demands on stakeholders. This paper ends with recommendations to harmonize regulations across Europe, ensuring that both innovation in agricultural waste management and practical pesticide reduction strategies are implemented in a way that supports farmers and producers, minimizing economic disruptions and encouraging sustainable agricultural practices.