Recycling of organic waste (OW) as fertilizer on farmland is a widespread practice that fosters sustainable development via resource reuse. However, the advantages of OW fertilization should be weighed against the potentially negative environmental impacts due to the presence of contaminants such as zinc (Zn). Current knowledge on the parameters controlling the environmental fate of Zn following OW application on cultivated soils is scant. We addressed this shortcoming by combining soil column experiments and Zn speciation characterization in OWs and amended soils. Soil column experiments were first carried out using two contrasted soils (sandy soil and sandy clay loam) that were amended with sewage sludge or poultry manure and cropped with lettuce. The soil columns were irrigated with identical amounts of water twice a week, and the leachates collected at the column outlet were monitored and analyzed. This scheme (OW application and lettuce crop cycle) was repeated for each treatment. Lettuce yields and Zn uptake were assessed at the end of each cycle. The soil columns were dismantled and seven soil layers were sampled and analyzed at the end of the second cycle (total experiment time: 12 weeks). X-ray absorption spectroscopy analyses were then conducted to assess Zn speciation in OW and OW-amended soils. The results of this study highlighted that (i) the fate of Zn in water–soil–plant compartments was similar, regardless of the type of soil and OW, (ii) >97.6% of the Zn input from OW accumulated in the soil surface layer, (iii) Zn uptake by lettuce increased with repeated OW applications, and (iv) no radical change in Zn speciation was observed at the end of the 12-week experiment, and phosphate was found to drive Zn speciation in both OW and amended soils (i.e., amorphous Zn-phosphate and Zn sorbed on hydoxylapatite). These results suggest that Zn speciation in OW is a key determinant controlling the environmental fate of this element in OW-amended soils.