This chapter reviews some of the methodologies and applications of N and C stable isotopes most useful to trace the fate of added organic or mineral material to the soil in natural and agricultural systems. Main results from two field experiments, one with N and the other with C stable isotopes, carried within the frame of MESCOSAGR project are presented. Three years research experiments aimed at evaluating the fate and flow rate of added N as 15N-compost in a maize-soil system and sorghum roots contribution to soil organic carbon evaluated by Natural Abundance Method, are carried out. The first year contribution of compost to plant nutrition was quantified to be about 20% of applied N, with decreasing values in the second and third subsequent years. A great variability of first year mineralization rates was found depending on the compost maturity and composition. Majority of changes in aggregate-associated SOM-15N consequently to compost amendment were observed in the soil macroaggregates. Estimation of the cumulative N-compost sequestrated in soil due to progressive amendments resulted in 34.2, 38.2 and 42.5 percent of total N -compost distributed the first (148 kg ha-1), the first and the second year (314 kg N ha-1), the three years of the research (442 kg ha-1), respectively. Research found that one year after sorghum cultivation the soil carbon plant-derived was between 8.24% to 21.29%, and values of 27.95% were reached after two and three years. The percentage of sorghum-derived carbon over the total surface of the soil organic carbon decreased with depth, and more markedly below 30 cm.