Conservation tillage is recognized as a sustainable management practice, however its combination with organic residues application still constitutes a challenge in some areas. A field trial was established in a semiarid agro-ecosystem to study the effects of different crop nutrient sources under minimum tillage (MT). Application of organic amendments at the beginning of a five-year crop rotation (ORG treatment) was evaluated and compared to the control plot where wheat was continuously grown with traditional mineral fertilization (MIN treatment). In addition to wheat yield and biomass, several soil properties were measured (pH, soil nutrients (i.e., Olsen P, exchangeable K, and mineral N), soil organic matter (i.e., C, N, C/N ratio), potentially mineralizable nitrogen, total microbial activity and heavy metals) throughout the 10-year study. The wheat yield was significantly higher under the ORG treatment than under the MIN, although climatic conditions (e.g., rainfall) exerted a great influence too. The organic amendments increased soil nutrients content mainly right after their application but the levels were adequate for the whole crop rotation. Plots under organic amendment application did not accumulate significantly more soil organic matter than those mineral-fertilized, probably due to the low protective capacity of coarse-textured soils. The application of organic amendments under MT resulted in a promising management agro-ecosystem compared to the mineral fertilized because crop nutrients came from organic wastes, no herbicides were applied while the yields were higher.