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The application of organic residues in agriculture helps to replenish soil organic carbon (OC), improve soil fertility and biodiversity, reinforce aggregate stability, and favour water infiltration. Moreover, its application as a soil amendment alters the fate of herbicides applied to the soil. The objective here was (i) to evaluate soil quality by determining the physicochemical and biological parameters of an agricultural soil (Soil) amended with green compost (Soil + GC) over an arable pea–wheat crop rotation in a short-term experiment; and (ii) to study the dissipation and persistence of iodosulfuron-methyl-sodium applied in field plots sown with winter wheat under real field conditions. The experimental field design consisted of 24 plots (10 m2) involving 12 with control and 12 with GC-amended soils. The plots were sown with pea after GC application (~11 t ha−1) in February 2023, and with winter wheat in October 2023. Iodosulfuron-methyl-sodium (Hussar® Plus, Bayer CropScience S.L., Barcelona, Spain) was applied in post-emergence at the agronomic dose (D1 = 176 mL ha−1) and double dose (D2 = 352 mL ha−1). Soil samples were taken from the plots to assess the soil physicochemical and biological parameters at six sampling times after GC application, with extraction and determination of residual herbicide and metabolite (metsulfuron-methyl) concentrations. In addition, the yield and characteristics of the pea and wheat grain crops were determined. The application of GC to the soil significantly increased pH (0.5 units by July 2024) and electrical conductivity (up to 5.2 times) compared to control soil, which remained constant throughout the experiment. The OC in Soil + GC increased by 40% in July 2024 compared to control soil. Total nitrogen content increased up to 2.0 and 1.3 times during the pea–wheat growing seasons in Soil + GC compared to unamended soil. Soil dehydrogenase activity, respiration, and biomass increased by up to 1.4, 2.2 and 1.4 times, respectively, in Soil + GC compared to unamended soil over the growing seasons. The soil microbial structure, determined by phospholipid fatty acid (PLFA) analysis, recorded no significant differences between the microbial groups in both soil treatments. A non-significant increase in pea and wheat yield was observed in Soil + GC compared to unamended soil. The results revealed an increase in the residual amounts of herbicide and metabolite, being slightly more persistent, with DT50 and DT90 values up to 1.6 times higher, in the Soil + GC plots over time. Much higher amounts of metabolite (DT50 = 24.8–29.7 days) than iodosulfuron-methyl (DT50 = 5.2–8.8 days) were found in all the treatments. This may be due to wheat plants intercepting the herbicide initially at the time of application in post-emergence, the rapid dissipation of the herbicide reaching the soil, and/or the higher persistence of the metabolite compared to that of the herbicide. Overall, the soil’s physicochemical and biological properties were improved in GC-amended soil, and organic amendment increased slightly the persistence of iodosulfuron-methyl-sodium and its metabolite in the soil.