Organic fertilizer applications can contribute to Zinc (Zn) biofortification of crops. An enriched stable isotope source tracing approach is a central tool to further determine the potential of this biofortification measure. Here, we assessed the use of the widely available quadrupole single-collector ICPMS (Q-ICPMS, analytical error = 1% relative standard deviation) and the less accessible but more precise multicollector ICPMS as reference instrument (MC-ICPMS, analytical error = 0.01% relative standard deviation) to measure enriched Zn stable isotope ratios in soil-fertilizer-plant systems. The isotope label was either applied to the fertilizer (direct method) or to the soil available Zn pool that was determined by isotope ratios measurements of the shoots that grew on labeled soils without fertilizer addition (indirect method). The latter approach is used to trace Zn that was added to soils with complex insoluble organic fertilizers that are difficult to label homogeneously. To reduce isobaric interferences during Zn isotope measurements, ion exchange chromatography was used to separate the Zn from the sample matrix. The 67Zn:66Zn isotope ratios altered from 0.148 at natural abundance to 1.561 in the fertilizer of the direct method and 0.218 to 0.305 in soil available Zn of the indirect method. Analysis of the difference (Bland-Altman) between the two analytical instruments revealed that the variation between 67Zn:66Zn isotope ratios measured with Q-ICPMS and MC-ICPMS were on average 0.08% [95% confidence interval (CI) = 0.68%]. The fractions of Zn derived from the fertilizer in the plant were on average 0.16% higher (CI = 0.49%) when analyzed with Q- compared to MC-ICPMS. The sample matrix had a larger impact on isotope measurements than the choice of analytical instrument, as non-purified samples resulted on average 5.79% (CI = 9.47%) higher isotope ratios than purified samples. Furthermore, the gain in analytical precision using MC-ICPMS instead of Q-ICPMS was small compared to the experimental precision. Thus, Zn isotope measurements of purified samples measured with Q-ICPMS is a valid method to trace Zn sources in soil-fertilizer-plant systems. For the indirect source tracing approach, we outlined strategies to sufficiently enrich the soil with Zn isotopes without significantly altering the soil available Zn pool.