Increasing soil organic carbon (SOC) in agroecosystems is a promising solution to simultaneously address climate change mitigation, adaptation, and food security. Yet, the best management practices that could achieve these goals remain to be identified. Here, we analyze the long-term effects of application of green manure, cereal straw, farmyard manure, and cattle slurry on SOC in a 37 year long field experiment in Switzerland. The treatment effects were compared against control conditions that received only optimal mineral fertilization. More specifically, this study aimed at evaluating the effect of organic amendments on SOC accumulation and distribution in different soil particle-size fractions by means of a set of indicators about organic matter quality (biological reactivity, humification index) and microbial activity (extracellular enzyme activities). In the absence of organic matter input, application of mineral fertilizers alone resulted in the lowest SOC content and the highest humification index of the bulk soil organic matter. Among the organic amendments, cereal straw, farmyard manure, and cattle slurry promoted a higher SOC content and a lower humification index due to an increase of SOC in the clay-size fraction. The annual C accrual reached 4.4‰ per year over 37 years with farmyard manure. The higher biological reactivity measured for the green manure and cereal straw amendments was associated with higher soil enzymatic activities, while C retention coefficients decreased by at least 2.5 times compared to animal-derived amendments. The low availability of nutrients in green manure and straw amendments as suggested by the high phosphatase and N-acetylglucosaminidase activities may indicate a reduction in C retention of organic matter inputs due to nutrient microbial mining with plant-derived amendments.