The effects of mineral fertilizers and organic amendments on soil properties, carbon (C) sequestration, and crop yields are studied in a 37-year field experiment, Phosphorus-Potassium-balanced design, in Switzerland. Treatments included a control (mineral fertilization) without nitrogen (N) fertilizers (Min-N0) and with optimal N (Min-Nopt) and 5 organic amendments (green manure [Gm], cereal straw [Str], fresh cattle manure in 2 doses 35 and 70 t ha(-1) [Ma35 and Ma70] and cattle slurry [Slu]) all receiving the same optimal N fertilization as Min-Nopt. All mineral and organic treatments received optimum P-K fertilization. Nitrogen fertilization (Min-Nopt vs. Min-N0) increased soil organic C, microbial activity, and microporosity but decreased pH, magnesium, and macroporosity. All organic treatments with optimal mineral N resulted in higher soil organic C content compared with Min-Nopt, however, these effects were significant only for the highest dose of manure. The organic amendments supplied 25% to 80% additional C input to the soil compared with Min-Nopt, and their amendment-C retention coefficients ranged from 1.6% (Gm) to 13.6% (Ma70). Chemical, physical, and biological soil properties were not or slightly significantly different among organic treatments. Nevertheless, soils fertilized with farmyard manure produced generally higher grain yield (up to 7.3%) compared with Min-Nopt whereas the opposite effect was noted for Gm (-2.2%) and Str (-5.2%) treatments due to their negative effect on N availability. In conclusion, Gm and Str treatments were as effectives as Ma35 and Slu treatments to prevent soil degradation but required higher chemical fertilizer to maintain crop yield.