Manure from animal production is commonly spread on agricultural soil as an organic fertiliser to provide macro and trace elements to crops. However, some trace elements can accumulate in the soil and become toxic to plants and microorganisms. These elements include copper (Cu) and zinc (Zn), which can be applied in large quantities when pig manure is spread. The feeding strategy and manure management (e.g. through treatment chains) are two mechanisms identified to better control the use of these elements, but their fate from the feed to the soil in pig production remains poorly documented. Better understanding the fate of Cu and Zn, as well as that of other trace and macro elements, along the feed – excreta – waste chain is required to develop alternative ways to reduce their environmental impacts. This dataset provides insight into the composition (Cu, Zn and other trace and macro elements) of organic products along two contrasting manure management chains: (1) only storage or (2) in-building separation, anaerobic digestion (AD) of solids, and digestate drying. Feed, raw slurry, liquid and solid phases after separation of the manure and AD products were sampled and then analysed to measure their total compound contents.