Agriculture is facing several challenges related to its sustainability. In this regard, the need to reduce its environmental impact related to the use of synthetic inputs and its potential role in mitigating global warming and climate change call for a review of crop management. In this context, and in the framework of achieving sustainable development goals, the use of organic fertilizers and bio-waste represents a valuable contribution to the agricultural transition towards a bioeconomy model by reducing the negative impacts of waste disposal. Farmyard manure, composts, digestate from agrifood processes, and biochar are, among organic fertilizers, commonly used to manage soils and support crop growth. These fertilizers can provide essential nutrients, improve structure, and enhance microbial activity, thus increasing soil fertility and agriculture sustainability. While organic fertilizers offer the benefits of soil fertility and plant nutrition, their impact on greenhouse gas (GHG) emissions is complex and varies depending on factors such as fertilizer type, soil conditions, and management practices. Although organic fertilizers may initially increase GHG emissions, they often lead to carbon sequestration in soils highlighting a negative C balance. Additionally, organic fertilizers promote a reduction in fossil fuel consumption used for synthetic fertilizer production, further contributing to GHG emissions’ reduction. Therefore, while organic fertilizers pose challenges in managing GHG emissions, their various benefits warrant careful consideration and strategic implementation in agricultural systems.