Isotope source tracing enables to accurately determine the fate of nutrients that are applied with fertilizers to soils. While this approach is well established for major nutrients such as nitrogen, it is not yet established for trace metals. Here, we aimed to determine the fate of the micronutrient zinc (Zn) and the contaminant cadmium (Cd) that were applied with an organic fertilizer to a soil-wheat system. A pot study was conducted in which wheat was grown on an alkaline soil. The soils received green manure and/or soluble Zn fertilizer and were compared with non-fertilized control treatments ( n = 4 experimental replicates). The green manure was labelled with the stable isotopes 67 Zn and 111 Cd. For an efficient sample throughput, a method was provided and validated to determine enriched stable isotope ratios ( 67 Zn: 66 Zn and 111 Cd: 110 Cd) and the Zn and Cd concentrations in one analytical run. To this end, single collector ICP-MS analyses and stable isotope mass balances calculations were combined. Applying this method revealed that the addition of green manure increased neither Zn nor Cd concentrations in wheat grains due to biomass dilution effects. Isotope source tracing showed that the largest fraction of these metals in the wheat shoots derived from the soil in all treatments (Zn 87-99 %, Cd 94-98 %). Moreover, the addition of green manure increased the transfer of Zn and Cd from soil to wheat by a factor 1.9 for both elements. This increased transfer was likely related to a nitrogen fertilization effect that increased root and shoot biomass and thereby the soil exploration of the wheat. This study demonstrated how the fate and dynamics of multiple trace metals can be efficiently determined in soil-fertilizer-crop systems using isotope source tracing.