Zinc (Zn) occurs naturally in soils, but spreading Zn-rich livestock manure on agricultural soils may lead to hazardous Zn levels. Interactions between exogenous Zn (from animal manure) and the soil matrix must be assessed to predict its behavior. We conducted soil density fractionation using sodium polytungstate solutions (LST) to isolate and identify the soil constituents and investigated their associations with Zn within five density fractions by characterizing the total organic carbon (TOC), mineralogy and Zn speciation. We analyzed a clayey Hapludox soil from a field experiment that had received pig slurry applications over an 11-year period, causing a 2-fold increase in the Zn concentration within the 0-5 cm layer relative to the control soil. Two density fractions with contrasting compositions were found: (i) a light fraction (<1.9 g cm − 3), which accounted for only ~5% of the bulk soil mass but contained the highest OM concentration; and (ii) a mineral-rich fraction (2.5-2.7 g cm − 3), which had a low OM concentration but accounted for ~80% of the soil mass. Zn in the control soil (no pig slurry application) was mostly (79.6%) in the mineral-rich fraction. Pig slurry applications increased the amount of Zn extracted by the fractionation solution to 16.6% and Zn in the organic-rich fraction to 13.2%, although the Zn in the mineral-rich fraction was still dominant (57.3%). The fraction extracted by the fractionation solution, the <1.9 g cm − 3 fraction and the 2.5-2.7 g cm − 3 fraction each accounted for roughly a third of the pig slurry-borne Zn in the amended soil. The results showed that 11 years of Zn-rich livestock manure application caused partial depletion of the clay sorption capacity of the soil, with the potential occurrence of Zn leaching in association with light density soil phases.