The intensive use of mineral (M) fertilizers may cause harm the environment via leaching or greenhouse gas emissions, destroy soil fertility as a consequence of loss of soil organic matter, and, due to their high price, they are economically unviable for producers. It is widely accepted that organic (O) fertilizers may deal with pressing challenges facing modern agriculture, even if farmers need to improve their knowledge for applying in fertilization programs. A meta-analysis approach has been adopted to evaluate the effects on soil organic carbon (SOC) and crop yield of O fertilizers, applied alone or in combination with mineral fertilizers (MO) under conventional (CT), reduced (RT), and no-tillage (NT) regimes. The analysis was performed in different climatic conditions, soil properties, crop species, and irrigation management. Organic fertilizers have a positive influence in increasing SOC compared with M (on average 12.9%), even if high values were observed under NT (20.6%). The results highlighted the need for flexible and environment-specific systems when considering organic fertilization subjected to different tillage regimes. Similarly, MO application showed a better crop yield response in CT and RT under coarse soils when compared with M fertilizer applied alone (on average 13.4 and 12.7%, respectively), while in medium-textured soils, CT and RT yielded better than NT under O fertilizers (9.5 and 11.2 vs. 2.5%, respectively). Among the crop species, legumes performed better when O fertilizers were adopted than M fertilizers (on average 15.2%), while among the other crop species, few differences were detected among the fertilization programs. Under irrigated systems, RT and NT led to higher productivity than CT, especially under MO treatments (on average 9.2 vs. 3.4%, respectively). The results highlighted the importance of the environmental and agronomical factors and how their understanding could affect the impact of these conservation farming practices on crop productivity to improve the sustainability of the farming system in a specific region.